In recent years, there has been a growing interest in research on Ceratozamia cycads, which has resulted in a significant increase in our understanding of their diversity. However, species complexes that have been tackled through integrative methodologies have exhibited a bias towards morphology over genealogy. Thus, there arises the necessity to reevaluate the Ceratozamia mexicana species complex using phylogeographic tools. For this purpose, we have employed the integrative taxonomic protocol Schlick-Steiner et al. (2010) put forth. This protocol delineates species as testable hypotheses, incorporating lines of evidence within a reproducible and falsifiable framework. The evaluated data encompassed (i) phylogenetic and molecular variance analyses, (ii) multivariate morphometric analyses, and (iii) analysis of climatic niches. Out of the 196 individuals from 13 studied populations, seven monophyletic groups were recovered. These groups were substantiated by multivariate morphometric analysis, revealing significant differences, and were further validated by niche divergence. These results underscore a ‘whole agreement’ across the three disciplines, thus providing robust support for acknowledging the species as distinct lineages. The species delimited by these lineages, encompassing phylogenetic, morphological, and environmental factors, correspond to C. brevifrons, C. delucana, C. decumbens, C. mexicana, C. moretti, C. tenuis, and a novel cryptic species, sister to the latter. Finally, this genealogical characterization will offer utility in the future for uncovering the genetic identity of the holotype of the type species within the Ceratozamia genus.