Java Heap vs Native Memory: What’s the Difference and Why It Matters

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When a Java application runs, it needs memory to function. But not all memories are the same. There are two key types of memories , Java Heap and Native Memory. Understanding the difference between them helps us diagnose and fix performance issues effectively. So understanding what they are, why they matter and what kind of trouble they get us into and how we can resolve them is crucial. This blog will just open the doorway for you to get an overall insight into it.

This short video breaks down the Java Heap vs Native Memory comparison and why both matter for your app’s performance.

What Is Java Heap Memory?

By definition, the Java heap is the area of memory used to store objects instantiated by applications running on the JVM. Say suppose in your application you are creating objects like ArrayList, HashMap, Customer, Account… all these objects are stored in the Java Heap Memory.

Think of it like a giant whiteboard that Java uses to scribble down all the things it’s working on. As long as the application is running, Java keeps adding to this board. When something is no longer needed, Java erases it. Thanks to Garbage Collection, which is the eraser that automatically removes unused objects to free up memory.

Fig: Java Memory

What Is Java Native Memory?

Java Native Memory is the portion of Java Process Memory that is outside of the Heap Memory. It contains metadata & low-level runtime structures that are required to execute the program effectively.

If I use the same analogy explained for Java Heap Memory, if it is something that the scribbled whiteboard, then Native Memory is the marker, the mounting frame, and even the screws holding the whiteboard to the wall. Java needs all of these to function properly, even though they’re not part of what’s actually written on the board. It contains following regions:

Metaspace: Metaspace is a region in native memory where the JVM stores class metadata, including class names, methods, fields, annotations, and constant pools. Every time your application loads a new class, either from third-party libraries or through dynamic generation (e.g., proxies, CGLIB), it consumes space in Metaspace. If the number of loaded classes keeps increasing and Metaspace reaches its configured or system-imposed limit, the JVM will throw an OutOfMemoryError: Metaspace.

Threads: Each Java thread requires its own native memory stack. When your application creates too many threads, especially in systems with limited native memory or in containers with memory limits, the operating system may be unable to allocate memory for new thread stacks. In such cases, the JVM throws OutOfMemoryError: unable to create new native thread. This isn’t a heap issue but a native memory exhaustion scenario due to thread overprovisioning.

Direct ByteBuffers: Direct ByteBuffers are created outside the regular Java heap using ByteBuffer.allocateDirect(). They are often used for high-performance I/O operations, because they offer better performance. But remember, these buffers consume native memory, which means their usage is not tracked by the garbage collector. If the total memory used by direct buffers exceeds the limit defined by -XX:MaxDirectMemorySize, the JVM throws an OutOfMemoryError: Direct buffer memory.

Code Cache: The Code Cache is a part of native memory region where the JVM stores machine code created by the Just-In-Time (JIT) compiler. In applications with a large codebase or frequent dynamic compilation, this cache can grow substantially over time, which can contribute to native memory pressure. If the Code Cache becomes full, you may see degraded performance due to disabled JIT compilation or rare cases of ‘OutOfMemoryError: CodeCache is full’. You can configure its size using -XX:ReservedCodeCacheSize.

JVM Internal Data Structures: The JVM also uses native memory for various internal subsystems such as garbage collector metadata, safepoint structures, and other runtime bookkeeping. These usually don’t throw a direct OutOfMemoryError, but they still add to the overall native memory usage. In memory-constrained environments like containers, the OS may forcibly shut down the JVM, when combined memory usage (heap + native) exceeds the allowed limit, resulting in OutOfMemoryError: Kill Process or Sacrifice Child.

JNI Allocations: JNI (Java Native Interface) allows Java code to interact with native libraries. These libraries can allocate memory independently of the JVM, which won’t be tracked or reclaimed by the garbage collector. If JNI memory usage grows unchecked, due to leaks or large native buffers, it can exhaust native memory. Depending on how the native code handles memory failures, this may cause a crash or lead to an unspecified OutOfMemoryError.

Common Memory Issues in Java Applications

Now that we have learnt the key difference, let’s move to the next section that shines light on the common memory issues related to these memories.

Java Heap OutOfMemoryError

As stated in the earlier section of the blog, the memory issues occur when the Java Heap is full and the Garbage Collector can’t free up space. It usually happens when too many objects are created and not released, or when the heap size is too small for the application’s workload.

It ultimately leads to this error ‘java.lang.OutOfMemoryError: Java heap space’ or ‘java.lang.OutOfMemoryError: GC overhead limit exceeded’ and we have already explained in detail how to identify and solve this problem. You can use tools like GCeasy, yCrash, HeapHero to monitor and troubleshoot these problems.

Native Memory OutOfMemoryError

This kind of memory error is harder to detect but it doesn’t mean it cannot be done. With the right tools you can troubleshoot anything and here’s some of the common memory errors listed and how they can be resolved.

You can use tools yCrash to monitor and troubleshoot NMT related problems.

Note: We recently hosted a webinar on ‘Java Native Memory Issues’, where we walked through real-world scenarios, debugging tips, and best practices to avoid memory-related crashes.

Key Differences Between Java Heap and Native Memory

While it appears on the surface-level that both are almost the same, there are some key differences, and here’s a table that can help you understand it even better:

Key Difference	Java Heap Memory	Native Memory
What is stored	Application Objects i.e., Customer, Account, List, etc.	Artifacts required to run the app: Threads, GC data, Metadata, Buffers
Who manages it	Managed by Garbage Collector	Managed by OS & JVM (JVM controls some parts like Metaspace)
How to configure	-Xmx	-XX:MaxMetaspaceSize,-XX:ReservedCodeCacheSize, -XX:MaxDirectMemorySize-Xss
Error When Exhausted	OutOfMemoryError: Java heap space OutOfMemoryError: GC overhead limit exceeded	OutOfMemoryError: MetaspaceOutOfMemoryError: unable to create new native threadOutOfMemoryError: Direct buffer memoryOutOfMemoryError: Code Cache full
Monitoring Tools	Heap dump analyzers: GCeasy, HeapHero, VisualVM	Native memory tracking: yCrash, NMT (Native Memory Tracking), OS-level tools
Cleanup Responsibility	Automatic via GC	Manual or system-managed (non-GC)
Troubleshooting Complexity	Easier to detect and fix using heap dumps	Harder to trace; issues often surface unexpectedly
Performance	Slower – involves object references and pointer traversal	Faster – more direct memory access

Why Knowing the Difference Helps You Fix Issues Faster

When performance issues or crashes occur in a Java application, the root cause often lies in memory, but not all memory problems are equal. Knowing whether the issue is in the Java Heap or Native Memory helps you avoid guesswork and quickly zero in on the right fix. So understanding the difference and what tools you can use to diagnose and fix them will be a huge advantage. It’s the first step toward smarter debugging and smoother performance.

GC easy – Universal Java GC Log Analyser