The Mayan Cichlid (Mayaheros urophthalmus) is usually considered to be a complex of 18 subspecies, most of which are endemic to the Yucatan Peninsula and were diagnosed by phenetic analyses based on traditional morphometrics and color pattern. However, morphological differences can be due to environmental conditions rather than taxonomic distinctiveness. We evaluated, by means of a geometric morphometric analysis, two hypotheses for shape differences in 20 natural populations of M. urophthalmus, including five subspecies recently raised to species status: M. alborus, M. cienagae, M. conchitae, M. mayorum, and M. zebra. The geographical distribution and three types of aquatic environment (River, Lagoon or Pond, and Cenote) were used as classificatory variables. In addition, a molecular analysis of two concatenated fragments of mitochondrial DNA (mtDNA), cytochrome b (cytb) and cytochrome oxidase subunit I (COI), showed genetic differentiation among some populations (F_ST = 0.36). Whereas the geometric morphometric analysis found significant differences among all aquatic environments, patterns of body shape of M. urophthalmus are more consistent with ecophenotypic variation than with genetic differentiation due to geographic isolation by distance. We think that there is currently no evidence to raise the traditionally recognized subspecies of M. urophthalmus to the species level.