The earliest diverging lineages in the subfamily Molossinae have not been well established. The genera Cheiromeles and Mormopterus have been found in separate studies to be the oldest lineage, however no previous studies using a molecular approach have included an analysis of sequence data from Cheiromeles and Mormopterus together in the same study. The objective of this study was to test the hypothesis that recombination activating gene 2 (Rag2) sequence data support the basal divergence of Cheiromeles in the Molossinae subfamily. Bayesian and Maximum Likelihood analyses of Rag2 sequences from 64 molossid bats (representing 13 genera, 31 species) and five outgroup taxa (Antrozous pallidus, Myotis daubentoni, M. velifer, M. yumanensis, and Natalus stramineus) obtained from GenBank resulted in the placement of Cheiromeles as the most basal lineage within a monophyletic Molossinae. Mormopterus was placed as sister to the rest of Molossinae (excluding Cheiromeles).