The Turks Island Boa (Epicrates c. chrysogaster) is endemic to the Turks and Caicos Islands and is currently known from only 11 islands. The subspecies has likely been extirpated from several islands in its historic range, and all remaining populations are threatened with extirpation owing to habitat loss, introduced feral predators, malicious killing, and vehicle strikes. To assist conservation efforts, we undertook a genetic analysis of 53 individual E. c. chrysogaster, representing five island populations, with the goal of identifying existing population structure and genetic diversity. For each snake sampled, we sequenced one mitochondrial and two nuclear genes, resulting in 1591 bp of sequence, and screened nine microsatellite loci. All individuals were found to be monomorphic at the four microsatellite loci that amplified, and only three individuals were found to vary (by a single nucleotide polymorphism) in either nuclear gene. Nine mitochondrial haplotypes were found, with a maximum sequence divergence of <1%. Taken together, these data indicate shallow genetic divergence in this subspecies, possibly owing to a lack of historical population structure and small population size when the Turks and Caicos Banks were each single islands during the last glacial maximum. Epicrates c. chrysogaster appears to represent a single evolutionarily significant unit, a significant finding suggesting that conservation strategies focusing on ecologically intact populations might be more appropriate than alternate strategies involving near-impossible reversal of declining populations on heavily disturbed islands. In addition, reintroduction programs would likely not disrupt any significant historical population structure.