We examined phylogenetic relationships among species of Liomys, including L. adspersus (Panamanian spiny pocket mouse), L. irroratus (Mexican spiny pocket mouse), L. pictus (painted spiny pocket mouse), L. salvini (Salvin's spiny pocket mouse), and L. spectabilis (Jaliscan spiny pocket mouse), several species of Heteromys, as well as representatives of other genera of heteromyids and 2 geomyids by using 1,140 base pairs of the mitochondrial cytochrome-b gene. Gene sequences analyzed under maximum-parsimony (MP), maximum-likelihood (ML), and Bayesian inference optimality criteria converged on essentially identical gene tree topologies. Liomys is paraphyletic relative to Heteromys and this relationship is well supported, with L. adspersus and L. salvini arranged as basal taxa relative to Heteromys. Our gene trees also recovered L. pictus as paraphyletic relative to L. spectabilis and these 2 taxa formed the sister group to L. irroratus. Constraint trees that held the genera Heteromys and Liomys as monophyletic (MP and ML criteria) were significantly longer or less likely (P < 0.009 and 0.046, respectively) than our optimal trees, whereas trees that arranged L. pictus as monophyletic relative to L. spectabilis were not significantly longer (P < 0.101) under the MP criterion, but were significantly less likely under the ML criterion (P < 0.020).