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The periodic number (PN) representation of the chemical systems, introduced by Dmitri Mendeleev, uncovers the fundamental principle of chemical similarity in a straightforward way. In this framework, the rows correspond to the principal quantum numbers of the elements’ electronic configurations when considered isolated atoms. This systematic arrangement allows for a deeper understanding of the relationships and patterns among the elements. In this study, we propose a novel strategy for structure type (prototype) prediction by utilizing the PN concept to identify possible modifications and phase stability of unexplored chemical systems. Our PN-based crystal structure prediction (PNcsp) program, which evaluates similarity through PN neighboring in the phase map, provides the most probable prototypes for unknown and unreported modifications of given phases in binary and higher order chemical systems. We applied PNcsp to 59 distinct chemical systems whose equimolar phases are indicated in the respective phase diagrams but lack accurate experimental structure determination. Our methodology identified 93 prototypes for these 59 equiatomic phases, of which 47 exhibit mechanical and dynamic stability. Notably, this approach discovered 19 entirely novel, fully stable polymorphic phases, thereby expanding the known landscape of potential materials. Furthermore, we demonstrated that this method is also effective for nonequimolar and higher order systems.