In most primates, one sex disperses from their natal group to reduce inbreeding. Habitat fragmentation may limit primates’ dispersal opportunities, however, which has implications for species survival. We examined the influence of fragmentation on genetic diversity in wild mantled howler monkeys (Alouatta palliata) at La Suerte, Costa Rica. The La Suerte region has seen increased fragmentation over the past decade as forest has been cleared for fruit plantations. We hypothesized that genetic diversity would be lowest in the forest edges compared to the interior because fragment boundaries restrict dispersal opportunities for edge groups. In summer 2015 we collected 96 fecal samples from the howler population and selected 20 samples each from the interior and the edge of the forest, respectively, using GIS locations of sample collection sites. To examine DNA polymorphism, we isolated DNA from these samples and used two primer sets to perform PCR amplifications of selected microsatellite loci (Apm01 and Ab06). Analysis of the amplified fragments was carried out using BigDye Terminator v3.1 sequencing and run on ABI 3730xl instrumentation. We recorded observed (Ho) and expected (He) heterozygosity values under Hardy-Weinberg equilibrium and derived F-statistics indices (FIS, FST and FIT) to quantify genetic variation in the sub-populations (interior vs. edge). We subsequently assessed the genetic health of the howler monkeys using these indices. Our results show that genetic diversity is highest at the edges of the forest and lowest in the interior. The inbreeding coefficient for the edge population was FIS = 0.45 and for the interior population FIS = 0.58, suggesting inbreeding is occurring in the interior of the forest. In addition, the overall inbreeding coefficient was FIT = 0.52, suggesting that the howler population as a whole is inbred. Overall, our results suggest that howler monkeys may be dispersing across open areas into neighboring fragments. These results may, however, be an artifact of our limited sample size. We therefore intend to analyze all samples collected in summer 2015 and those that will be collected in summer 2016. The results we present here are the initial stage of what we anticipate will become a long-term project examining the influence of habitat fragmentation on dispersal and genetic diversity in wild mantled howler monkeys.