Sequences of two mitochondrial genes (385 base pairs of cytochrome b and approximately 520 base pairs of 16S DNA) were gathered for 26 taxa of the Middle American plethodontid salamander genera Nototriton and Oedipina and from three outgroup members of the tribe Bolitoglossini. Phylogenetic analyses of these data reveal well-supported cladistic structure and demonstrate the paraphyly of the moss salamanders of the genus Nototriton, which includes two well-defined clades. One clade, the sister taxon of Oedipina, corresponding to the Costa Rican and Honduran species of the picadoi, richardi, and barbouri groups, retains the name Nototriton. A new name is required for the second clade, the sister taxon of Oedipina plus Nototriton (sensu stricto). This clade, which we name Cryptotriton, is well supported morphologically and includes the species of the nasalis and adelos groups. A new species of Nototriton from Monteverde, Costa Rica, is described as Nototriton gamezi. Species of Oedipina fall into two clades that we treat as subgenera. Oedipina (sensu stricto) includes the longer-bodied, generally more slender and darker colored species and is the more speciose clade. Oedopinola includes the shorter-bodied, generally more robust and lighter-colored species. Two new species of the latter clade are described, Oedipina maritima from the lowlands of northwestern Panamá, and Oedipina savagei, from uplands of southwestern Costa Rica.