In this manuscript we presented MAYGEN, an open-source constitutional isomer generator completely written in Java. MAYGEN generates constitutional isomer spaces exhaustively and avoids isomorphic structures during the generation using the principles of orderly canonical graph generation. We presented extensive testing of MAYGEN against two alternative solutions: MAYGEN outperforms the current best single-thread structure generator OMG by one order of magnitude and is only marginally slower than the fastest in the current state-of-the-art software MOLGEN. We expect MAYGEN to be a starting point for further developments in the area of chemical structure generation by the open source, open science community.