Pairwise, two- and three-way Mantel tests were used to evaluate a null hypothesis of no significant covariation when morphological features of three cyprinid fish taxa of the genus Gila were compared. Tests involved ecological conditions and past and present hydrography in the Gila River Basin of western North America. A vicariance hypothesis was the only model statistically proficient in explaining diversity of fish phenotypes. Of paleohydrographic reconstructions compared, those of the mid-Miocene and Pliocene epochs were significantly associated with present-day distributions of phenotypes. Of these, the Pliocene was paramount.