Despite dramatic growth in the field of primate genomics over the past decade, studies of primate population and conservation genomics in the wild have been hampered due to the difficulties inherent in studying non-model organisms and endangered species, such as lack of a reference genome and current challenges in de novo primate genome assembly. Here, we used Restriction-site Associated DNA (RAD) sequencing to develop a population-based SNP panel for the Ugandan red colobus (P. rufomitratus tephrosceles), which is a highly threatened monkey due to habitat loss. We analyzed blood samples from 24 individuals from Kibale National Park (Uganda) using single-end RAD sequencing. We obtained 70,773,857 reads, of which 58,814,906 passed the filtering steps. Using the program STACKS v. 1.11 we identified 113,376 loci, of which 50,558 were polymorphic and had a mean observed heterozygosity of 0.25. These data will be used to study the effects of habitat fragmentation on genomic diversity, dispersal, and disease transmission in this species. Our approach provides a good example of the potential of RAD sequencing in studies of wild primate populations.