Currently, the genetic population structure of only 3 green turtle, Chelonia mydas, rookeries is used to categorize the Eastern Caribbean grouping of the South Atlantic distinct population segment. Tissue samples were collected from 66 nesting green turtles on the East End beaches of St. Croix, US Virgin Islands from 2012 to 2015, and we sequenced ∼ 800 base pairs of the mitochondrial DNA (mtDNA) control region to characterize the genetic structure and test for differentiation with the adjacent Buck Island rookery. The haplotypes CmA5.1, CmA5.2, and CmA3.1 were identified on the East End beaches. Results of pairwise tests for differentiation were mixed, with frequency-based F_ST failing to detect differentiation at the p < 0.05 threshold (F_ST = 0.01148, p = 0.18503), and an exact test indicating significant differentiation (p = 0.02146). The detection of CmA3.1 and not CmA16.1 within the East End beaches adds to the haplotype diversity previously observed in the Eastern Caribbean region and suggests that genetic diversity has been underestimated in previous studies. Further investigation including mitogenomic markers and nuclear DNA analyses would provide additional clarity as to the population structure in this region.