Captive populations can play a significant role in threatened and endangered species management. An important consideration when developing and managing captive populations, however, is the maintenance of genetic diversity to ensure that adequate variation exists to avoid the negative consequences of inbreeding. In this investigation, we compared genetic diversity patterns within captive and wild populations of the federally endangered Quino checkerspot butterfly (Euphydryas editha quino Behr [Lepidoptera: Nymphalidae]), a taxon with a restricted distribution to chaparral and sage shrublands within Riverside and San Diego counties, California. Our analyses revealed that medium to high-frequency alleles from the wild populations were also present in the captive populations. While there was no significant difference in genetic diversity as quantified by expected heterozygosity, the captive populations showed tendencies toward significantly lower allelic richness than their wild counterparts. Given that alleles from the wild populations were occasionally not detected in captive populations, periodic incorporation of new wild specimens into the captive population would help ensure that allelic diversity is maintained to the extent possible. If performed in advance, genetic surveys of wild populations may provide the clearest insights regarding the number of individuals needed in captivity to adequately reflect wild populations.