Abstract: Geological and climatic events frequently represent the primary explanations to describe evolutionary processes among species. Freshwater fishes have been used previously as models to uncover evolutionary and historical biogeographic patterns in central Mexico, hydrologic systems and biotas. Xenotoca variata (Cyprinodontiformes: Goodeidae) is one of the most widely distributed species across central Mexico. The species represents a highly dimorphic and sexually selective species. In this study, the phylogenetic and phylogeographic patterns of populations of X. variata, using one mitochondrial locus (cytb) and three nuclear loci (S7, RHO, and RAG1), were described in order to understand the evolutionary history of the species throughout its distributional range. Two well‐defined and highly supported clades were recovered with all analyses and genes studied, with an estimated divergence time of ca. 2.42 Mya, corroborating the existence of an independent evolutionary unit in Cuitzeo Lake and its recognition as a putative new species. Also, a phylogeographic structure in two genes was found within the widely distributed clades. The role played by climate change events and geological history as well as the possible influence of reproductive traits in the phylogeographic pattern of the species are discussed.

Key words: biogeography, Cuitzeo Lake, endemic fish, geological history, sexual selection