Costa Rica is within the Mesoamerican biodiversity hotspot and has about 53 native species of small mammals. This high diversity, along with recent records of new species and indications of cryptic genetic diversity, suggest that application of the DNA barcoding approach would be worthwhile. Here we used 131 tissue samples of small mammals from multiple localities in Costa Rica and sequenced the complete mitochondrial cytochrome b (1140 bp). These samples represented 17 recognized species and two taxa of uncertain status. The new sequence data were supplemented with previously published data from INSDC. Our phylogenetic analyses are consistent with and extend upon recent revisions in Heteromys, Peromyscus and Reithrodontomys and suggest possible new cryptic forms within what are currently named Melanomys chrysomelas, Nyctomys sumichrasti and Proechimys semispinosus. The previously named “Heteromys sp” is indeed likely a new species requiring a full taxonomic description. Moreover, we found new localities for previously described species substantiating recent taxonomic surveys and field guides for the small mammals of Costa Rica. To confirm the presence of cryptic species and major genetic forms in Heteromys, Peromyscus, Reithrodontomys, Melanomys, Nyctomys and Proechimys there needs to be greater sampling, additional genetic markers, morphometrics and other studies. Scotinomys also shows interesting phylogenetic subdivision, requiring further investigation.
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