Taxonomy of the live-bearing fish of the genus Ilyodon Eigenmann, 1907 (Goodeidae), in Mexico, is controversial, with morphology and mitochondrial genetic analyses in disagreement about the number of valid species. The present study accumulated a comprehensive DNA sequences dataset of 98 individuals of all Ilyodon species and mitochondrial and nuclear loci to reconstruct the evolutionary history of the genus. Phylogenetic inference produced five clades, one with two sub-clades, and one clade including three recognized species. Genetic distances in mitochondrial genes (cytb: 0.5%¿2.1%; coxI: 0.5%¿1.1% and d-loop: 2.3%¿10.2%) were relatively high among main clades, while, as expected, nuclear genes showed low variation (0.0%¿0.2%), with geographic concordance and few shared haplotypes among river basins. High genetic structure was observed among clades and within basins. Our genetic analyses, applying the priority principle, suggest the recognition only of Ilyodon whitei and Ilyodon furcidens, with I. cortesae relegated to an invalid species, the populations of which belong to I. whitei

We thank the Ministerio de Economía y Competitividad for funding the project (CGL-2013 41375-P).

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