PhyloSystemX is a computational tool designed to reconstruct ancestral biological interaction networks by integrating phylogenetic species trees with modern interaction data. While systems biologists commonly use networks to represent complex biological interactions, contemporary network analysis alone cannot reveal the evolutionary history that shaped these systems. PhyloSystemX addresses this gap by implementing parsimony-based algorithms (Dollo and Sankoff adjusted algorithm) to infer both ancestral vertices (homology groups) and their interactions across evolutionary time. Unlike tools limited to specific interaction types, PhyloSystemX can analyze any network whose vertices can be labeled with homology identifiers, including protein–protein interactions, gene co-expression networks, and metabolic regulation systems. By inferring ancestral networks, researchers can uncover evolutionarily conserved functional modules, identify lineage-specific innovations, and explore how biological systems adapt over time. The current implementation assumes vertical inheritance of traits, with limitations regarding introgression, hybridization, and horizontal gene transfer that future versions may address.