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Rapid anthropogenic land use change threatens the primary habitat of the Chestnut short-tailed bat ( Carollia castanea ) throughout much of its range. Information on population genetic structure can inform management strategies for this widespread frugivorous bat, and effective protection of  C. castanea  will also benefit the more than 20 mutualistic plant species of which this bat is the primary seed disperser. To facilitate understanding of population genetic structure in this species, fourteen novel microsatellite markers were developed using restriction-site-associated DNA libraries and Illumina sequencing and tested on 28 individuals from 13 locations in Costa Rica. These are the first microsatellite markers developed for  C. castanea . All loci were polymorphic, with number of alleles ranging from 2–11 and average observed heterozygosity of 0.631. Markers were also cross-amplified in three additional frugivorous bat species threatened by habitat loss and fragmentation: Sowell’s short-tailed bat ( Carollia sowelli ), Seba’s short-tailed bat ( Carollia perspicillata ), and the Jamaican fruit bat ( Artibeus jamaicensis ), and 10, 11, and 8 were polymorphic, respectively.

peerj

Development and characterization of fourteen novel microsatellite markers for the chestnut short-tailed fruit bat (Carollia castanea), and cross-amplification to related species