Hm.
Finally, I used the bouncy Castle dll to create certificates. Using this method, you can set the issuer name.
This is the complete code for creating x509Certificate and for storage in the repository
private X509Certificate2 GeneratePFXFile(string certificate,string company,string email,string state,string locality,string username,string country) { X509Certificate2 cert = null; try { var kpgen = new RsaKeyPairGenerator(); kpgen.Init(new KeyGenerationParameters(new SecureRandom(new CryptoApiRandomGenerator()), 2048)); var kp = kpgen.GenerateKeyPair(); var gen = new X509V3CertificateGenerator(); var certName = new X509Name("CN=" + certificate); var issuer = new X509Name("C="+country+",O="+company+",OU=LBC Mundial Corp.USA,E="+email+",L="+locality+",ST="+state); var serialNo = BigInteger.ProbablePrime(120, new Random()); gen.SetSerialNumber(serialNo); gen.SetSubjectDN(certName); gen.SetIssuerDN(issuer); gen.SetNotAfter(DateTime.Now.AddYears(50)); gen.SetNotBefore(DateTime.Now); gen.SetSignatureAlgorithm("MD5WithRSA"); gen.SetPublicKey(kp.Public); gen.AddExtension( X509Extensions.AuthorityKeyIdentifier.Id, false, new AuthorityKeyIdentifier( SubjectPublicKeyInfoFactory.CreateSubjectPublicKeyInfo(kp.Public), new GeneralNames(new GeneralName(certName)), serialNo)); gen.AddExtension( X509Extensions.ExtendedKeyUsage.Id, false, new ExtendedKeyUsage(new ArrayList() { new DerObjectIdentifier("1.3.6.1.5.5.7.3.1") })); var newCert = gen.Generate(kp.Private); byte[] pfx = DotNetUtilities.ToX509Certificate(newCert).Export(System.Security.Cryptography.X509Certificates.X509ContentType.Pfx, (string)null); X509Store store = new X509Store((StoreName)StoreName.TrustedPeople, (StoreLocation)StoreLocation.LocalMachine); store.Open(OpenFlags.ReadWrite); cert = new X509Certificate2(pfx,(string)null, X509KeyStorageFlags.PersistKeySet | X509KeyStorageFlags.MachineKeySet); store.Add(cert); store.Close(); } catch (Exception ex) { ShowError(ex.Message); return null; } return cert; }