The Miami blue butterfly, Cyclargus thomasi bethunebakeri (Comstock and Huntington) (Lepidoptera: Lycaenidae) is state-endangered in Florida and a candidate for federal listing. Extant colonies exist in a metapopulation structure and are limited to a single location, Bahia Honda State Park in the lower Florida Keys. A captive breeding colony was initiated from Bahia Honda stock to safeguard the taxon and to provide organisms for reintroduction. Wing fragment samples from both wild and captive colony specimens were collected for DNA extraction and microsatellite analyses. These genetic data were used to infer population structure, overall genetic variability, and gene flow within the extant metapopulation for 2005 and 2006. Genetic variability was also assessed for several generations of the captive colony. Comparisons of microsatellite data between captive colony and wild-caught individuals reveal differences in allelic diversity and overall genetic variability. The conservation implications of using captive-bred individuals for reintroduction are discussed.