California's Central Valley has undergone large-scale agricultural development fragmenting the desert ecosystem and putting many species, such as the giant kangaroo rat (Dipodomys ingens), at risk of extinction. Dispersal and population structuring must be considered when designing and implementing conservation efforts. We aimed to noninvasively identify potential dispersal behaviors that may affect mate choice. Fecal samples were collected from the Carrizo Plain in the southern Central Valley from two trapping grids approximately 100 meters apart. We genotyped samples at 15 microsatellite loci and a newly developed sex marker. We recovered genotypes from 145 (of 200) samples and identified 83 distinct individuals. Next, we examined individuals' relatedness and geographic position to determine the species' population structure. The mean distance between 1st, 2nd, and 3rd order relatives were 77, 52, and 132 meters respectively with a significant difference only between 2nd and 3rd order pairings. 1st order pairings followed a bimodal distribution with relatives being either near (~10-20m) or far (~200m) apart. We examined the sex of individuals in 1st order pairings to assess if sex bias explains the bimodal dispersal distance. Male-male 1st order pairings were found both near and far, suggesting that male offspring do not uniformly disperse long distances.