How to retrieve/compute an X509 certificate's thumbprint in Java?

The SHA-1 hash of the DER encoding of the certificate is what .NET is getting with X509Certificate2.Thumbprint.

As noted on the remarks on MSDN:

The thumbprint is dynamically generated using the SHA1 algorithm and does not physically exist in the certificate. Since the thumbprint is a unique value for the certificate, it is commonly used to find a particular certificate in a certificate store.

Java's standard library doesn't provide the thumbprint directly, but you can get it like this:

DatatypeConverter.printHexBinary(
        MessageDigest.getInstance("SHA-1").digest(
                cert.getEncoded())).toLowerCase();

Here's a full worked example using a conveniently accessible PEM file:

  1. Create stackoverflow.crt.pem:

    -----BEGIN CERTIFICATE-----
    MIIHHjCCBgagAwIBAgIQDhG71w1UtxDQxvVAtrUspDANBgkqhkiG9w0BAQsFADBw
    MQswCQYDVQQGEwJVUzEVMBMGA1UEChMMRGlnaUNlcnQgSW5jMRkwFwYDVQQLExB3
    d3cuZGlnaWNlcnQuY29tMS8wLQYDVQQDEyZEaWdpQ2VydCBTSEEyIEhpZ2ggQXNz
    dXJhbmNlIFNlcnZlciBDQTAeFw0xNjA1MjEwMDAwMDBaFw0xOTA4MTQxMjAwMDBa
    MGoxCzAJBgNVBAYTAlVTMQswCQYDVQQIEwJOWTERMA8GA1UEBxMITmV3IFlvcmsx
    HTAbBgNVBAoTFFN0YWNrIEV4Y2hhbmdlLCBJbmMuMRwwGgYDVQQDDBMqLnN0YWNr
    ZXhjaGFuZ2UuY29tMIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAr0YD
    zscT5i6T2FaRsTGNCiLB8OtPXu8N9iAyuaROh/nS0kRRsN8wUMk1TmgZhPuYM6oF
    S377V8W2LqhLBMrPXi7lnhvKt2DFWCyw38RrDbEsM5dzVGErmhux3F0QqcTI92zj
    VW61DmE7NSQLiR4yonVpTpdAaO4jSPJxn8d+4p1sIlU2JGSk8LZSWFqaROc7KtXt
    lWP4HahNRZtdwvL5dIEGGNWx+7B+XVAfY1ygc/UisldkA+a3D2+3WAtXgFZRZZ/1
    CWFjKWJNMAI6ZBAtlbgSNgRYxdcdleIhPLCzkzWysfltfiBmsmgz6VCoFR4KgJo8
    Gd3MeTWojBthM10SLwIDAQABo4IDuDCCA7QwHwYDVR0jBBgwFoAUUWj/kK8CB3U8
    zNllZGKiErhZcjswHQYDVR0OBBYEFFrBQmPCYhOznZSEqjIeF8tto4Z7MIIB6AYD
    VR0RBIIB3zCCAduCEyouc3RhY2tleGNoYW5nZS5jb22CEXN0YWNrb3ZlcmZsb3cu
    Y29tghMqLnN0YWNrb3ZlcmZsb3cuY29tgg1zdGFja2F1dGguY29tggtzc3RhdGlj
    Lm5ldIINKi5zc3RhdGljLm5ldIIPc2VydmVyZmF1bHQuY29tghEqLnNlcnZlcmZh
    dWx0LmNvbYINc3VwZXJ1c2VyLmNvbYIPKi5zdXBlcnVzZXIuY29tgg1zdGFja2Fw
    cHMuY29tghRvcGVuaWQuc3RhY2thdXRoLmNvbYIRc3RhY2tleGNoYW5nZS5jb22C
    GCoubWV0YS5zdGFja2V4Y2hhbmdlLmNvbYIWbWV0YS5zdGFja2V4Y2hhbmdlLmNv
    bYIQbWF0aG92ZXJmbG93Lm5ldIISKi5tYXRob3ZlcmZsb3cubmV0gg1hc2t1YnVu
    dHUuY29tgg8qLmFza3VidW50dS5jb22CEXN0YWNrc25pcHBldHMubmV0ghIqLmJs
    b2dvdmVyZmxvdy5jb22CEGJsb2dvdmVyZmxvdy5jb22CGCoubWV0YS5zdGFja292
    ZXJmbG93LmNvbYIVKi5zdGFja292ZXJmbG93LmVtYWlsghNzdGFja292ZXJmbG93
    LmVtYWlsMA4GA1UdDwEB/wQEAwIFoDAdBgNVHSUEFjAUBggrBgEFBQcDAQYIKwYB
    BQUHAwIwdQYDVR0fBG4wbDA0oDKgMIYuaHR0cDovL2NybDMuZGlnaWNlcnQuY29t
    L3NoYTItaGEtc2VydmVyLWc1LmNybDA0oDKgMIYuaHR0cDovL2NybDQuZGlnaWNl
    cnQuY29tL3NoYTItaGEtc2VydmVyLWc1LmNybDBMBgNVHSAERTBDMDcGCWCGSAGG
    /WwBATAqMCgGCCsGAQUFBwIBFhxodHRwczovL3d3dy5kaWdpY2VydC5jb20vQ1BT
    MAgGBmeBDAECAjCBgwYIKwYBBQUHAQEEdzB1MCQGCCsGAQUFBzABhhhodHRwOi8v
    b2NzcC5kaWdpY2VydC5jb20wTQYIKwYBBQUHMAKGQWh0dHA6Ly9jYWNlcnRzLmRp
    Z2ljZXJ0LmNvbS9EaWdpQ2VydFNIQTJIaWdoQXNzdXJhbmNlU2VydmVyQ0EuY3J0
    MAwGA1UdEwEB/wQCMAAwDQYJKoZIhvcNAQELBQADggEBAAzJAMGSdKoX1frdqNlN
    iXu8Gcbsm/DxWMXpcTXlZn8s+/qQQoc+/3o0CK3C8/j9n5DmsYa88P6Ntt5ysDs+
    b0ynXFva4CAEyKaoPM4SIpOjwfWBRSUOqAIkQO2/LhKBwT/EnpaIHIKGnI0UdXLQ
    oDfkMDg6mgJsEBsKdKF5EfEX7iU3NO5xVJPJE8/R0btLAdYwxB9S6fSpCXGe2HqQ
    D101O/7/4MWNdFSbfdDSFcn5oEm+idimrqiNrF5knmuJy4qPBkL7thNuGK6rvYCF
    ZJM03ZEZhkQmn2jG/7LgjfwZmvfcITeADCpylf88bL+lf+vxe6cCl9CyqWgBDpsI
    xpE=
    -----END CERTIFICATE-----
    
  2. Create X509.java:

    import javax.xml.bind.DatatypeConverter;
    import java.io.FileInputStream;
    import java.io.FileNotFoundException;
    import java.security.MessageDigest;
    import java.security.NoSuchAlgorithmException;
    import java.security.cert.CertificateEncodingException;
    import java.security.cert.CertificateException;
    import java.security.cert.CertificateFactory;
    import java.security.cert.X509Certificate;
    
    public final class X509 {
        public static void main(String[] args)
                throws FileNotFoundException, CertificateException, NoSuchAlgorithmException {
            FileInputStream is = new FileInputStream(args[0]);
            CertificateFactory certificateFactory = CertificateFactory.getInstance("X.509");
            X509Certificate cert = (X509Certificate) certificateFactory.generateCertificate(is);
            String thumbprint = getThumbprint(cert);
            System.out.println(thumbprint);
        }
    
        private static String getThumbprint(X509Certificate cert)
                throws NoSuchAlgorithmException, CertificateEncodingException {
            MessageDigest md = MessageDigest.getInstance("SHA-1");
            byte[] der = cert.getEncoded();
            md.update(der);
            byte[] digest = md.digest();
            String digestHex = DatatypeConverter.printHexBinary(digest);
            return digestHex.toLowerCase();
        }
    }
    
  3. Compile the program with Java 8:

    javac X509.java
    

    Or Java 9 - due to modular JDK/JPMS - DataTypeConverter is not in java.base, but java.xml.bind, so you need to explicitly depend on it during your build:

    javac --add-modules java.xml.bind X509.java
    

    Otherwise, on Java 9, you get this when you try to build it:

    X509.java:3: error: package javax.xml.bind is not visible
            import javax.xml.bind.DatatypeConverter;
            ^
            (package javax.xml.bind is declared in module java.xml.bind, which is not in the module graph)
            1 error
    
  4. Run it with Java 8:

    java X509 stackoverflow.crt.pem
    

    In Java 9 - due to modular JDK/JPMS - DataTypeConverter is not in java.base, but java.xml.bind, so you need to explicitly depend on it when running your program:

    java --add-modules java.xml.bind X509 stackoverflow.crt.pem
    

    Otherwise, on Java 9, you get this when you try to run it:

    Exception in thread "main" java.lang.NoClassDefFoundError: javax/xml/bind/DatatypeConverter
        at X509.getThumbPrint(X509.java:29)
        at X509.main(X509.java:19)
        Caused by: java.lang.ClassNotFoundException: javax.xml.bind.DatatypeConverter
        at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)
        at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:185)
        at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:496)
        ... 2 more
    
  5. Get the expected output:

    47adb03649a2eb18f63ffa29790818349a99cab7
    

Using Apache Commons Codec you can do:

DigestUtils.sha1Hex(cert.getEncoded())

One-liner using Google's Guava

Hashing.sha256().hashBytes(cert.getEncoded()).toString();

You can generate the thumbprint by using the openssl command, so example if you have the pem format of the certificate in a file (file.txt)

then:

cat file.txt | openssl x509 -sha1 -fingerprint - this would generate the same thumbprint