The jaguarundi (Puma yagouaroundi) is a Neotropical felid that ranges from northern Mexico to South America. The population trend for jaguarundis is declining, yet much remains unknown about their ecology. We live-trapped 11 jaguarundis during 1991–2004 in Tamaulipas, Mexico, and we collected blood for genetic analyses. Our objectives were to 1) estimate neutral diversity using microsatellite and mitochondrial (mtDNA) markers, 2) estimate potentially adaptive diversity in coat coloration via the melanocortin-1 receptor gene (MC1R), and 3) provide recommendations on the use of genetic markers for noninvasive studies. We observed moderate levels of heterozygosity (HE = 0.49, SD = 0.22) and number of alleles (A = 4.00, SD = 1.65) at 12 feline microsatellite loci. The probability of identifying 2 different jaguarundis as the same individual was low using only 4–7 loci (P(ID) < 0.001 and P(ID)sib < 0.01, respectively). We observed one mtDNA haplotype, indicating no mtDNA diversity. However, we documented diversity with the MC1R assay. The frequency of the melanistic mutation (gray phenotype) was 0.33, whereas, the frequency was 0.67 for the ancestral allele (red phenotype). Microsatellite diversity of our sampled jaguarundis was less than that of sympatric populations of ocelots (Leopardus pardalis) in Tamaulipas; however, mtDNA diversity was much lower. The frequency of the melanistic mutation was lower in our sample than was previously reported in captive jaguarundis. Our microsatellite loci provided adequate diversity to implement noninvasive genetic tools to better understand the ecology of the elusive jaguarundi. To our knowledge, this work is the first genetic evaluation of wild jaguarundis and provides baseline information for future research and conservation. © 2013 The Wildlife Society.