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We analyzed DNA sequence variation in the cytochrome-b gene and intron 7 of the nuclear fibrinogen, B beta polypeptide gene for 45 specimens of the bat genus Micronycteris, including all currently recognized species except M. sanborni. Phylogenetic analyses of both data sets supported 4 primary lineages within Micronycteris, which we recognize as subgenera: Leuconycteris new subgenus (M. brosseti), Micronycteris Gray (M. megalotis, M. microtis, M. matses, and M. giovanniae), Schizonycteris new subgenus (M. minuta, M. schimdtorum, and M. sanborni), and Xenoctenes Miller (M. hirsuta). Although we provisionally recognize the current alpha taxonomy within Micronycteris, our results did not support monophyly of M. microtis as the name is currently applied. Our results further indicate that cryptic species probably exist within the taxa currently recognized as M. megalotis and M. minuta and possibly M. hirsuta. Additional studies, including thorough geographic sampling and detailed morphological and molecular data sets, are necessary to test our genealogic hypotheses and assess the biodiversity within Micronycteris.