This chapter presents the data structures in GPenSIM. Some of the data structures are simple as they represent the basic elements such as a place, transition, token, token colors, and resource. The other data structures are large (and sometimes complex) as they represent static Petri net graph (‘spng’), Petri net structure with initial dynamics (‘pni’), and Petri Net run-time structure (‘PN’); these structures combine the basic Petri net structure with colors and resources (in Colored Petri nets) and Modules (in Modular Petri nets).