Chromosomal rearrangements have been hypothesized to be the cause of reproductive isolation leading to speciation in diverse taxa. One model for chromosomal speciation, speciation by monobrachial centric fusions, is thought to apply to various groups of mammals, including members of the bat genus Rhogeessa (Chiroptera: Vespertilionidae). Specifically, this model has been proposed to account for diversification within the R. tumida species complex. This species group exhibits a high degree of karyotypic variation, with little to no morphological differentiation between species. By examining phylogenetic data derived from DNA sequences of maternal, paternal and bi-parentally inherited markers, I investigate phylogenetic relationships of species within Rhogeessa and test expectations of the model of speciation by monobrachial centric fusions on members of the R. tumida complex. If chromosomal fusions caused speciation in Rhogeessa, I expect to see patterns of reproductive isolation between species differing by monobrachial fusions, and therefore each chromosomal form should be a monophyletic group. My data generally follow this pattern, with the exception of potential evidence for historical hybridization between R. tumida (2n = 34) and R. aeneus (2n = 32), where none is expected under the model. There is no evidence, however, of ongoing or recent hybridization between any taxa differing karyotypically. Moreover, the speciation model predicts that all populations which contain the same set of chromosomal fusions should freely interbreed, if chromosomal rearrangements are the sole cause for reproductive isolation. My data also show an exception to this prediction based on the observation of multiple genetic lineages of karyotypically identical R. tumida (2n = 34). This observation indicates that chromosomal differences cannot account for genetic diversification between the different lineages of R. tumida. Phylogeographic analyses indicate that lineages within this species could have diverged due to differences in habitat preferences. Overall, these data are generally consistent with speciation having occurred via reproductive isolation caused by chromosomal fusions. However, it does not appear that these rearrangements have caused complete reproductive isolation due to the evidence consistent with historical hybridization between Rhogeessa tumida and R. aeneus. The chromosomal mechanism is also not likely to be the only means by which diversification has taken place in Rhogeessa. Geographic factors have apparently influenced genetic divergence as well.