diff --git a/src/ipsec/_ipsec.8.in b/src/ipsec/_ipsec.8.in
index 210d74ef8..0aef8c031 100644
--- a/src/ipsec/_ipsec.8.in
+++ b/src/ipsec/_ipsec.8.in
@@ -210,15 +210,18 @@ flushes and rereads all secrets defined in \fIipsec.secrets\fP.
 .
 .TP
 .B "rereadcacerts"
-reads all certificate files contained in the \fI/etc/ipsec.d/cacerts\fP
-directory and adds them to the list of Certification Authority (CA)
-certificates.
+removes previously loaded CA certificates, reads all certificate files
+contained in the \fI/etc/ipsec.d/cacerts\fP directory and adds them to the list
+of Certification Authority (CA) certificates. This does not affect certificates
+explicitly defined in a
+.BR ipsec.conf (5)
+ca section, which may be separately updated using the \fBupdate\fP command.
 .
 .TP
 .B "rereadaacerts"
-reads all certificate files contained in the \fI/etc/ipsec.d/aacerts\fP
-directory and adds them to the list of Authorization Authority (AA)
-certificates.
+removes previously loaded AA certificates, reads all certificate files
+contained in the \fI/etc/ipsec.d/aacerts\fP directory and adds them to the list
+of Authorization Authority (AA) certificates.
 .
 .TP
 .B "rereadocspcerts"
diff --git a/src/libcharon/plugins/stroke/stroke_ca.c b/src/libcharon/plugins/stroke/stroke_ca.c
index f8026875f..b470b81c6 100644
--- a/src/libcharon/plugins/stroke/stroke_ca.c
+++ b/src/libcharon/plugins/stroke/stroke_ca.c
@@ -119,6 +119,84 @@ static void ca_section_destroy(ca_section_t *this)
 	free(this);
 }
 
+/**
+ * Data for the certificate enumerator
+ */
+typedef struct {
+	private_stroke_ca_t *this;
+	certificate_type_t cert;
+	key_type_t key;
+	identification_t *id;
+} cert_data_t;
+
+/**
+ * destroy cert_data
+ */
+static void cert_data_destroy(cert_data_t *data)
+{
+	data->this->lock->unlock(data->this->lock);
+	free(data);
+}
+
+/**
+ * filter function for certs enumerator
+ */
+static bool certs_filter(cert_data_t *data, ca_section_t **in,
+						 certificate_t **out)
+{
+	public_key_t *public;
+	certificate_t *cert = (*in)->cert;
+
+	if (data->cert == CERT_ANY || data->cert == cert->get_type(cert))
+	{
+		public = cert->get_public_key(cert);
+		if (public)
+		{
+			if (data->key == KEY_ANY || data->key == public->get_type(public))
+			{
+				if (data->id && public->has_fingerprint(public,
+											data->id->get_encoding(data->id)))
+				{
+					public->destroy(public);
+					*out = cert;
+					return TRUE;
+				}
+			}
+			public->destroy(public);
+		}
+		else if (data->key != KEY_ANY)
+		{
+			return FALSE;
+		}
+		if (data->id == NULL || cert->has_subject(cert, data->id))
+		{
+			*out = cert;
+			return TRUE;
+		}
+	}
+	return FALSE;
+}
+
+METHOD(credential_set_t, create_cert_enumerator, enumerator_t*,
+	private_stroke_ca_t *this, certificate_type_t cert, key_type_t key,
+	identification_t *id, bool trusted)
+{
+	enumerator_t *enumerator;
+	cert_data_t *data;
+
+	INIT(data,
+		.this = this,
+		.cert = cert,
+		.key = key,
+		.id = id,
+	);
+
+	this->lock->read_lock(this->lock);
+	enumerator = this->sections->create_enumerator(this->sections);
+	return enumerator_create_filter(enumerator, (void*)certs_filter, data,
+									(void*)cert_data_destroy);
+}
+
 /**
  * data to pass to create_inner_cdp
  */
@@ -438,7 +516,7 @@ stroke_ca_t *stroke_ca_create(stroke_cred_t *cred)
 		.public = {
 			.set = {
 				.create_private_enumerator = (void*)return_null,
-				.create_cert_enumerator = (void*)return_null,
+				.create_cert_enumerator = _create_cert_enumerator,
 				.create_shared_enumerator = (void*)return_null,
 				.create_cdp_enumerator = _create_cdp_enumerator,
 				.cache_cert = (void*)nop,
@@ -456,4 +534,3 @@ stroke_ca_t *stroke_ca_create(stroke_cred_t *cred)
 
 	return &this->public;
 }
-
diff --git a/src/libcharon/plugins/stroke/stroke_cred.c b/src/libcharon/plugins/stroke/stroke_cred.c
index 0dc03ec16..5e423f1de 100644
--- a/src/libcharon/plugins/stroke/stroke_cred.c
+++ b/src/libcharon/plugins/stroke/stroke_cred.c
@@ -70,10 +70,20 @@ struct private_stroke_cred_t {
 	char *secrets_file;
 
 	/**
-	 * credentials
+	 * credentials: end entity certs, attribute certs, CRLs, etc.
 	 */
 	mem_cred_t *creds;
 
+	/**
+	 * CA certificates
+	 */
+	mem_cred_t *cacerts;
+
+	/**
+	 * Attribute Authority certificates
+	 */
+	mem_cred_t *aacerts;
+
 	/**
 	 * ignore missing CA basic constraint (i.e. treat all certificates in
 	 * ipsec.conf ca sections and ipsec.d/cacerts as CA certificates)
@@ -231,7 +241,7 @@ METHOD(stroke_cred_t, load_ca, certificate_t*,
 		}
 		DBG1(DBG_CFG, "  loaded ca certificate \"%Y\" from '%s'",
 			 cert->get_subject(cert), filename);
-		return this->creds->add_cert_ref(this->creds, TRUE, cert);
+		return this->creds->get_cert_ref(this->creds, cert);
 	}
 	return NULL;
 }
@@ -373,134 +383,184 @@ METHOD(stroke_cred_t, load_pubkey, certificate_t*,
 	return NULL;
 }
 
+/**
+ * Load a CA certificate  from disk
+ */
+static void load_x509_ca(private_stroke_cred_t *this, char *file)
+{
+	certificate_t *cert;
+
+	if (this->force_ca_cert)
+	{	/* treat certificate as CA cert even it has no CA basic constraint */
+		cert = lib->creds->create(lib->creds, CRED_CERTIFICATE, CERT_X509,
+								  BUILD_FROM_FILE, file,
+								  BUILD_X509_FLAG, X509_CA, BUILD_END);
+	}
+	else
+	{
+		cert = lib->creds->create(lib->creds, CRED_CERTIFICATE, CERT_X509,
+								  BUILD_FROM_FILE, file, BUILD_END);
+	}
+	if (cert)
+	{
+		x509_t *x509 = (x509_t*)cert;
+
+		if (!(x509->get_flags(x509) & X509_CA))
+		{
+			DBG1(DBG_CFG, "  ca certificate \"%Y\" lacks ca basic constraint, "
+				 "discarded", cert->get_subject(cert));
+			cert->destroy(cert);
+		}
+		else
+		{
+			DBG1(DBG_CFG, "  loaded ca certificate \"%Y\" from '%s'",
+				 cert->get_subject(cert), file);
+			this->cacerts->add_cert(this->cacerts, TRUE, cert);
+		}
+	}
+	else
+	{
+		DBG1(DBG_CFG, "  loading ca certificate from '%s' failed", file);
+	}
+}
+
+/**
+ * Load AA certificate with flags from disk
+ */
+static void load_x509_aa(private_stroke_cred_t *this, char *file)
+{
+	certificate_t *cert;
+
+	cert = lib->creds->create(lib->creds, CRED_CERTIFICATE, CERT_X509,
+							  BUILD_FROM_FILE, file,
+							  BUILD_X509_FLAG, X509_AA, BUILD_END);
+	if (cert)
+	{
+		DBG1(DBG_CFG, "  loaded AA certificate \"%Y\" from '%s'",
+			 cert->get_subject(cert), file);
+		this->aacerts->add_cert(this->aacerts, TRUE, cert);
+	}
+	else
+	{
+		DBG1(DBG_CFG, "  loading AA certificate from '%s' failed", file);
+	}
+}
+
+/**
+ * Load a certificate with flags from disk
+ */
+static void load_x509(private_stroke_cred_t *this, char *file, x509_flag_t flag)
+{
+	certificate_t *cert;
+
+	/* for all other flags, we add them to the certificate. */
+	cert = lib->creds->create(lib->creds, CRED_CERTIFICATE, CERT_X509,
+							  BUILD_FROM_FILE, file,
+							  BUILD_X509_FLAG, flag, BUILD_END);
+	if (cert)
+	{
+		DBG1(DBG_CFG, "  loaded certificate \"%Y\" from '%s'",
+			 cert->get_subject(cert), file);
+		this->creds->add_cert(this->creds, TRUE, cert);
+	}
+	else
+	{
+		DBG1(DBG_CFG, "  loading certificate from '%s' failed", file);
+	}
+}
+
+/**
+ * Load a CRL from a file
+ */
+static void load_x509_crl(private_stroke_cred_t *this, char *file)
+{
+	certificate_t *cert;
+
+	cert = lib->creds->create(lib->creds, CRED_CERTIFICATE, CERT_X509_CRL,
+							  BUILD_FROM_FILE, file, BUILD_END);
+	if (cert)
+	{
+		this->creds->add_crl(this->creds, (crl_t*)cert);
+		DBG1(DBG_CFG, "  loaded crl from '%s'",  file);
+	}
+	else
+	{
+		DBG1(DBG_CFG, "  loading crl from '%s' failed", file);
+	}
+}
+
+/**
+ * Load an attribute certificate from a file
+ */
+static void load_x509_ac(private_stroke_cred_t *this, char *file)
+{
+	certificate_t *cert;
+
+	cert = lib->creds->create(lib->creds, CRED_CERTIFICATE, CERT_X509_AC,
+							  BUILD_FROM_FILE, file, BUILD_END);
+	if (cert)
+	{
+		DBG1(DBG_CFG, "  loaded attribute certificate from '%s'", file);
+		this->creds->add_cert(this->creds, FALSE, cert);
+	}
+	else
+	{
+		DBG1(DBG_CFG, "  loading attribute certificate from '%s' failed", file);
+	}
+}
+
 /**
  * load trusted certificates from a directory
  */
 static void load_certdir(private_stroke_cred_t *this, char *path,
 						 certificate_type_t type, x509_flag_t flag)
 {
+	enumerator_t *enumerator;
 	struct stat st;
 	char *file;
 
-	enumerator_t *enumerator = enumerator_create_directory(path);
-
-	if (!enumerator)
+	enumerator = enumerator_create_directory(path);
+	if (enumerator)
+	{
+		while (enumerator->enumerate(enumerator, NULL, &file, &st))
+		{
+			if (!S_ISREG(st.st_mode))
+			{
+				/* skip special file */
+				continue;
+			}
+			switch (type)
+			{
+				case CERT_X509:
+					if (flag & X509_CA)
+					{
+						load_x509_ca(this, file);
+					}
+					else if (flag & X509_AA)
+					{
+						load_x509_aa(this, file);
+					}
+					else
+					{
+						load_x509(this, file, flag);
+					}
+					break;
+				case CERT_X509_CRL:
+					load_x509_crl(this, file);
+					break;
+				case CERT_X509_AC:
+					load_x509_ac(this, file);
+					break;
+				default:
+					break;
+			}
+		}
+		enumerator->destroy(enumerator);
+	}
+	else
 	{
 		DBG1(DBG_CFG, "  reading directory failed");
-		return;
 	}
-
-	while (enumerator->enumerate(enumerator, NULL, &file, &st))
-	{
-		certificate_t *cert;
-
-		if (!S_ISREG(st.st_mode))
-		{
-			/* skip special file */
-			continue;
-		}
-		switch (type)
-		{
-			case CERT_X509:
-				if (flag & X509_CA)
-				{
-					if (this->force_ca_cert)
-					{	/* treat this certificate as CA cert even it has no
-						 * CA basic constraint */
-						cert = lib->creds->create(lib->creds,
-										CRED_CERTIFICATE, CERT_X509,
-										BUILD_FROM_FILE, file, BUILD_X509_FLAG,
-										X509_CA, BUILD_END);
-					}
-					else
-					{
-						cert = lib->creds->create(lib->creds,
-										CRED_CERTIFICATE, CERT_X509,
-										BUILD_FROM_FILE, file, BUILD_END);
-					}
-					if (cert)
-					{
-						x509_t *x509 = (x509_t*)cert;
-
-						if (!(x509->get_flags(x509) & X509_CA))
-						{
-							DBG1(DBG_CFG, "  ca certificate \"%Y\" lacks "
-								 "ca basic constraint, discarded",
-								 cert->get_subject(cert));
-							cert->destroy(cert);
-							cert = NULL;
-						}
-						else
-						{
-							DBG1(DBG_CFG, "  loaded ca certificate \"%Y\" "
-								 "from '%s'", cert->get_subject(cert), file);
-						}
-					}
-					else
-					{
-						DBG1(DBG_CFG, "  loading ca certificate from '%s' "
-									  "failed", file);
-					}
-				}
-				else
-				{	/* for all other flags, we add them to the certificate. */
-					cert = lib->creds->create(lib->creds,
-										CRED_CERTIFICATE, CERT_X509,
-										BUILD_FROM_FILE, file,
-										BUILD_X509_FLAG, flag, BUILD_END);
-					if (cert)
-					{
-						DBG1(DBG_CFG, "  loaded certificate \"%Y\" from '%s'",
-									  cert->get_subject(cert), file);
-					}
-					else
-					{
-						DBG1(DBG_CFG, "  loading certificate from '%s' "
-									  "failed", file);
-					}
-				}
-				if (cert)
-				{
-					this->creds->add_cert(this->creds, TRUE, cert);
-				}
-				break;
-			case CERT_X509_CRL:
-				cert = lib->creds->create(lib->creds,
-										  CRED_CERTIFICATE, CERT_X509_CRL,
-										  BUILD_FROM_FILE, file,
-										  BUILD_END);
-				if (cert)
-				{
-					this->creds->add_crl(this->creds, (crl_t*)cert);
-					DBG1(DBG_CFG, "  loaded crl from '%s'",  file);
-				}
-				else
-				{
-					DBG1(DBG_CFG, "  loading crl from '%s' failed", file);
-				}
-				break;
-			case CERT_X509_AC:
-				cert = lib->creds->create(lib->creds,
-										  CRED_CERTIFICATE, CERT_X509_AC,
-										  BUILD_FROM_FILE, file,
-										  BUILD_END);
-				if (cert)
-				{
-					this->creds->add_cert(this->creds, FALSE, cert);
-					DBG1(DBG_CFG, "  loaded attribute certificate from '%s'",
-								  file);
-				}
-				else
-				{
-					DBG1(DBG_CFG, "  loading attribute certificate from '%s' "
-								  "failed", file);
-				}
-				break;
-			default:
-				break;
-		}
-	}
-	enumerator->destroy(enumerator);
 }
 
 METHOD(stroke_cred_t, cache_cert, void,
@@ -1321,6 +1381,8 @@ METHOD(stroke_cred_t, reread, void,
 	{
 		DBG1(DBG_CFG, "rereading ca certificates from '%s'",
 			 CA_CERTIFICATE_DIR);
+		this->cacerts->clear(this->cacerts);
+		lib->credmgr->flush_cache(lib->credmgr, CERT_X509);
 		load_certdir(this, CA_CERTIFICATE_DIR, CERT_X509, X509_CA);
 	}
 	if (msg->reread.flags & REREAD_OCSPCERTS)
@@ -1334,6 +1396,8 @@ METHOD(stroke_cred_t, reread, void,
 	{
 		DBG1(DBG_CFG, "rereading aa certificates from '%s'",
 			 AA_CERTIFICATE_DIR);
+		this->aacerts->clear(this->aacerts);
+		lib->credmgr->flush_cache(lib->credmgr, CERT_X509);
 		load_certdir(this, AA_CERTIFICATE_DIR, CERT_X509, X509_AA);
 	}
 	if (msg->reread.flags & REREAD_ACERTS)
@@ -1359,7 +1423,11 @@ METHOD(stroke_cred_t, add_shared, void,
 METHOD(stroke_cred_t, destroy, void,
 	private_stroke_cred_t *this)
 {
+	lib->credmgr->remove_set(lib->credmgr, &this->aacerts->set);
+	lib->credmgr->remove_set(lib->credmgr, &this->cacerts->set);
 	lib->credmgr->remove_set(lib->credmgr, &this->creds->set);
+	this->aacerts->destroy(this->aacerts);
+	this->cacerts->destroy(this->cacerts);
 	this->creds->destroy(this->creds);
 	free(this);
 }
@@ -1392,9 +1460,13 @@ stroke_cred_t *stroke_cred_create()
 								"%s.plugins.stroke.secrets_file", SECRETS_FILE,
 								lib->ns),
 		.creds = mem_cred_create(),
+		.cacerts = mem_cred_create(),
+		.aacerts = mem_cred_create(),
 	);
 
 	lib->credmgr->add_set(lib->credmgr, &this->creds->set);
+	lib->credmgr->add_set(lib->credmgr, &this->cacerts->set);
+	lib->credmgr->add_set(lib->credmgr, &this->aacerts->set);
 
 	this->force_ca_cert = lib->settings->get_bool(lib->settings,
 						"%s.plugins.stroke.ignore_missing_ca_basic_constraint",
diff --git a/src/libcharon/plugins/stroke/stroke_cred.h b/src/libcharon/plugins/stroke/stroke_cred.h
index f6fbb96d3..9434629ef 100644
--- a/src/libcharon/plugins/stroke/stroke_cred.h
+++ b/src/libcharon/plugins/stroke/stroke_cred.h
@@ -50,10 +50,13 @@ struct stroke_cred_t {
 	void (*reread)(stroke_cred_t *this, stroke_msg_t *msg, FILE *prompt);
 
 	/**
-	 * Load a CA certificate, and serve it through the credential_set.
+	 * Load a CA certificate.
+	 *
+	 * This method does not add the loaded CA certificate to the internal
+	 * credentail set, but returns it only.
 	 *
 	 * @param filename		file to load CA cert from
-	 * @return				reference to loaded certificate, or NULL
+	 * @return				loaded certificate, or NULL
 	 */
 	certificate_t* (*load_ca)(stroke_cred_t *this, char *filename);
 
diff --git a/src/libstrongswan/credentials/sets/mem_cred.c b/src/libstrongswan/credentials/sets/mem_cred.c
index d8f568d36..7ad011b5e 100644
--- a/src/libstrongswan/credentials/sets/mem_cred.c
+++ b/src/libstrongswan/credentials/sets/mem_cred.c
@@ -192,6 +192,24 @@ METHOD(mem_cred_t, add_cert_ref, certificate_t*,
 	return add_cert_internal(this, trusted, cert);
 }
 
+METHOD(mem_cred_t, get_cert_ref, certificate_t*,
+	private_mem_cred_t *this, certificate_t *cert)
+{
+	certificate_t *cached;
+
+	this->lock->write_lock(this->lock);
+	if (this->untrusted->find_first(this->untrusted,
+									(linked_list_match_t)certificate_equals,
+									(void**)&cached, cert) == SUCCESS)
+	{
+		cert->destroy(cert);
+		cert = cached->get_ref(cached);
+	}
+	this->lock->unlock(this->lock);
+
+	return cert;
+}
+
 METHOD(mem_cred_t, add_crl, bool,
 	private_mem_cred_t *this, crl_t *crl)
 {
@@ -736,6 +754,7 @@ mem_cred_t *mem_cred_create()
 			},
 			.add_cert = _add_cert,
 			.add_cert_ref = _add_cert_ref,
+			.get_cert_ref = _get_cert_ref,
 			.add_crl = _add_crl,
 			.add_key = _add_key,
 			.add_shared = _add_shared,
diff --git a/src/libstrongswan/credentials/sets/mem_cred.h b/src/libstrongswan/credentials/sets/mem_cred.h
index d0dd51da1..3ce815abc 100644
--- a/src/libstrongswan/credentials/sets/mem_cred.h
+++ b/src/libstrongswan/credentials/sets/mem_cred.h
@@ -58,6 +58,18 @@ struct mem_cred_t {
 	certificate_t *(*add_cert_ref)(mem_cred_t *this, bool trusted,
 								   certificate_t *cert);
 
+	/**
+	 * Get an existing reference to the same certificate.
+	 *
+	 * Searches for the same certficate in the set, and returns a reference
+	 * to it, destroying the passed certificate. If the passed certificate
+	 * is not found, it is just returned.
+	 *
+	 * @param cert			certificate to look up
+	 * @return				the same certificate, potentially different instance
+	 */
+	certificate_t* (*get_cert_ref)(mem_cred_t *this, certificate_t *cert);
+
 	/**
 	 * Add an X.509 CRL to the credential set.
 	 *