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A central part of the JHI5 is the Java class hdf.hdf5lib.H5. The H5class calls the standard (i.e., `native' code) HDF5 library, with native methods for most of the HDF5 functions. In general, there is one native method call for each function in the HDF5 API, with similar arguments. Consult the HDF5 reference manual for details of the C API. (HDF5 API Specification)

The Java HDF5 Interface consists of Java classes and dynamically linked native libraries. The Java classes declare native methods, and the library contains C functions which implement the native methods. The C functions call the standard HDF5 library, which is linked as part of the same library on most platforms. The Java HDF5 Interface also translates between Java and C arrays, and converts error codes from the HDF5 C library to Java Exceptions.