Previous understanding of the relationships among genera of bats in the family Molossidae was based largely on phenetic analyses of morphological data. Relationships among the genera of this family have not been tested with molecular data and, thus, the objective of this study was to construct a phylogeny of representative members of free-tailed bats using DNA sequence data from 1 mitochondrial locus (Nicotinamide adenine dinucleotide dehydrogenase subunit 1 [ND1]) and 3 nuclear loci (dentin matrix protein 1 exon 6 [DMP1], beta fibrinogen intron 7 [βFIB], and recombination activating gene 2 [RAG2]) for members of the subfamily Molossinae and outgroups from the families Vespertilionidae and Natalidae. Data for each gene were analyzed separately using maximum-likelihood and Bayesian methods and also analyzed in a single combined analysis of a total of 3,216 base pairs. Divergence times were estimated from the combined data set using BEAST analysis. Few intergeneric relationships were significantly supported by mitochondrial data; however, monophyly of most genera was supported. Nuclear results supported a Chaerephon–Mops clade; a New World clade consisting of Eumops, Molossus, Promops, Molossops (including Neoplatymops), Cynomops, and Nyctinomops; and a basal divergence for Cheiromeles. Divergence analysis suggested a Paleocene origin for the family and a split between molossids in the Old World and New World around 29 million years ago. Generally, relationships recovered in our analyses reflected biogeographic proximity of species and did not support the hypotheses of relationship proposed by morphological data.