First of all, to actually understand the concept behind clone better I recommend the answer to the question: How to properly override clone method?
Regarding the source code you have put into your question:
native means here, that this is a method which is not implemented with Java, but with another language, often C or C++. It's still part of the JVM, hence you can find the actual implementation in the OpenJDK™ Source Release in the
"openjdk/hotspot/src/share/vm/prims/jvm.cpp":539 JVM_ENTRY(jobject, JVM_Clone(JNIEnv* env, jobject handle)) JVMWrapper("JVM_Clone"); Handle obj(THREAD, JNIHandles::resolve_non_null(handle)); const KlassHandle klass (THREAD, obj->klass()); JvmtiVMObjectAllocEventCollector oam; . . . JVM_END