Wildlife face ever-increasing threats from emerging pathogens, many that also cause disease in humans. Genetic diversity plays a central role in buffering populations against the effects of parasites and pathogens. The ability to isolate genes related directly to disease susceptibility and understanding how those genes evolve is important for designing successful and cost-effective conservation programs. We are investigating the relationship between diversity in six immune system genes and the parasite community of black-tailed prairie dogs. We live-trapped black-tailed prairie dogs (Cynomys ludovicianus) on three colonies weekly June-November 2007 and April-November 2008. We captured 358 prairie dogs, of which 212 are unique individuals, from three colonies during 2006-2007. For each of these individuals we have one tissue sample, as well as fecal and blood samples and total fleas from all capture events. We have the same information from an additional 222 captures (208 unique individuals that were not also captured by us in 2007-2008) from eight colonies during 2005-2006. In total, we have 420 unique individuals from eight colonies collected over four years. This research will provide insight into the evolution of resistance and susceptibility in black-tailed prairie dogs and provide valuable conservation genetic information. This is the first comprehensive survey of black-tailed prairie dog parasites on the Shortgrass Steppe Long Term Ecological Research site.