Monitors locked in native method (via JNI MonitorEnter) doesn't show up directly in jstack (unless there's a deadlock), because monitors are only shown with a stack frame, and native frames don't show up in plain old jstack.

build.sh

g++ -I $JAVA_HOME/include/ -I $JAVA_HOME/include/linux/ -fPIC -shared -o libfoo.so foo.cpp

command_prompt

[sajia@211 test_native_monitorenter]$ java -version
java version "1.6.0_30"
Java(TM) SE Runtime Environment (build 1.6.0_30-b12)
OpenJDK 64-Bit Server VM (build 20.0-b12-internal-fastdebug, mixed mode)
[sajia@211 test_native_monitorenter]$ jps
12676 Jps
12651 Main
[sajia@211 test_native_monitorenter]$ jstack -l 12651
2012-03-26 16:51:08
Full thread dump OpenJDK 64-Bit Server VM (20.0-b12-internal-fastdebug mixed mode):

"Attach Listener" daemon prio=10 tid=0x00002aaaafcbd800 nid=0x31b2 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
   JavaThread state: _thread_blocked
Thread: 0x00002aaaafcbd800  [0x31b2] State: _call_back _has_called_back 1 _at_poll_safepoint 0
   JavaThread state: _thread_blocked

   Locked ownable synchronizers:
        - None

"Low Memory Detector" daemon prio=10 tid=0x00002aaab8007800 nid=0x3180 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
   JavaThread state: _thread_blocked
Thread: 0x00002aaab8007800  [0x3180] State: _at_safepoint _has_called_back 0 _at_poll_safepoint 0
   JavaThread state: _thread_blocked

   Locked ownable synchronizers:
        - None

"C2 CompilerThread1" daemon prio=10 tid=0x00002aaab8004800 nid=0x317f waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
   JavaThread state: _thread_blocked
Thread: 0x00002aaab8004800  [0x317f] State: _at_safepoint _has_called_back 0 _at_poll_safepoint 0
   JavaThread state: _thread_blocked

   Locked ownable synchronizers:
        - None

"C2 CompilerThread0" daemon prio=10 tid=0x00002aaab8001000 nid=0x317e waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
   JavaThread state: _thread_blocked
Thread: 0x00002aaab8001000  [0x317e] State: _at_safepoint _has_called_back 0 _at_poll_safepoint 0
   JavaThread state: _thread_blocked

   Locked ownable synchronizers:
        - None

"Signal Dispatcher" daemon prio=10 tid=0x00002aaaafc83000 nid=0x317d runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
   JavaThread state: _thread_blocked
Thread: 0x00002aaaafc83000  [0x317d] State: _at_safepoint _has_called_back 0 _at_poll_safepoint 0
   JavaThread state: _thread_blocked

   Locked ownable synchronizers:
        - None

"Finalizer" daemon prio=10 tid=0x00002aaaafc53800 nid=0x317c in Object.wait() [0x000000004199a000]
   java.lang.Thread.State: WAITING (on object monitor)
   JavaThread state: _thread_blocked
Thread: 0x00002aaaafc53800  [0x317c] State: _at_safepoint _has_called_back 0 _at_poll_safepoint 0
   JavaThread state: _thread_blocked
        at java.lang.Object.wait(Native Method)
        - waiting on <0x0000000758601300> (a java.lang.ref.ReferenceQueue$Lock)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
        - locked <0x0000000758601300> (a java.lang.ref.ReferenceQueue$Lock)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
        at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

   Locked ownable synchronizers:
        - None

"Reference Handler" daemon prio=10 tid=0x00002aaaafc51800 nid=0x317b in Object.wait() [0x0000000041899000]
   java.lang.Thread.State: WAITING (on object monitor)
   JavaThread state: _thread_blocked
Thread: 0x00002aaaafc51800  [0x317b] State: _at_safepoint _has_called_back 0 _at_poll_safepoint 0
   JavaThread state: _thread_blocked
        at java.lang.Object.wait(Native Method)
        - waiting on <0x00000007586011d8> (a java.lang.ref.Reference$Lock)
        at java.lang.Object.wait(Object.java:485)
        at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
        - locked <0x00000007586011d8> (a java.lang.ref.Reference$Lock)

   Locked ownable synchronizers:
        - None

"main" prio=10 tid=0x00000000420a5000 nid=0x316c runnable [0x0000000040871000]
   java.lang.Thread.State: RUNNABLE
   JavaThread state: _thread_blocked
Thread: 0x00000000420a5000  [0x316c] State: _call_back _has_called_back 1 _at_poll_safepoint 0
   JavaThread state: _thread_blocked
        at Foo.spinWait(Foo.java:13)
        at Foo.lockMe(Native Method)
        at Foo.bar(Foo.java:7)
        at Main.main(Main.java:3)

   Locked ownable synchronizers:
        - None

"VM Thread" prio=10 tid=0x00002aaaafc49000 nid=0x317a runnable 

"GC task thread#0 (ParallelGC)" prio=10 tid=0x00000000420bd000 nid=0x316d runnable 

"GC task thread#1 (ParallelGC)" prio=10 tid=0x00000000420bf000 nid=0x316e runnable 

"GC task thread#2 (ParallelGC)" prio=10 tid=0x00000000420c1800 nid=0x316f runnable 

"GC task thread#3 (ParallelGC)" prio=10 tid=0x00000000420c3800 nid=0x3170 runnable 

"GC task thread#4 (ParallelGC)" prio=10 tid=0x00000000420c5800 nid=0x3171 runnable 

"GC task thread#5 (ParallelGC)" prio=10 tid=0x00000000420c7800 nid=0x3172 runnable 

"GC task thread#6 (ParallelGC)" prio=10 tid=0x00000000420c9800 nid=0x3173 runnable 

"GC task thread#7 (ParallelGC)" prio=10 tid=0x00000000420cb800 nid=0x3174 runnable 

"GC task thread#8 (ParallelGC)" prio=10 tid=0x00000000420cd800 nid=0x3175 runnable 

"GC task thread#9 (ParallelGC)" prio=10 tid=0x00000000420cf800 nid=0x3176 runnable 

"GC task thread#10 (ParallelGC)" prio=10 tid=0x00000000420d1800 nid=0x3177 runnable 

"GC task thread#11 (ParallelGC)" prio=10 tid=0x00000000420d3800 nid=0x3178 runnable 

"GC task thread#12 (ParallelGC)" prio=10 tid=0x00000000420d5800 nid=0x3179 runnable 

"VM Periodic Task Thread" prio=10 tid=0x00002aaab8013800 nid=0x3181 waiting on condition 

Compiler thread printing unimplemented.

JNI global references: 873

[sajia@211 test_native_monitorenter]$ 

foo.cpp

#include "Foo.h"

void JNICALL Java_Foo_lockMe(JNIEnv* env, jobject self) {
  env->MonitorEnter(self);

  jmethodID mid = env->GetMethodID(env->GetObjectClass(self), "spinWait", "()V");
  env->CallVoidMethod(self, mid);

  env->MonitorExit(self);
}

Foo.h

/* DO NOT EDIT THIS FILE - it is machine generated */
#include <jni.h>
/* Header for class Foo */

#ifndef _Included_Foo
#define _Included_Foo
#ifdef __cplusplus
extern "C" {
#endif
/*
 * Class:     Foo
 * Method:    lockMe
 * Signature: ()V
 */
JNIEXPORT void JNICALL Java_Foo_lockMe
  (JNIEnv *, jobject);

#ifdef __cplusplus
}
#endif
#endif

Foo.java

public class Foo {
  static {
    System.loadLibrary("foo");
  }

  public void bar() {
    lockMe();
  }

  private void spinWait() {
    while (true) {
      // burn some CPU
      int i = 0;
      i++;
    }
  }

  public native void lockMe();
}

Main.java

public class Main {
  public static void main(String[] args) {
    new Foo().bar();
  }
}