Green sea turtle conservation benefits from knowledge of population connectivity across different life stages. Green turtles are usually managed at the level of genetically discrete rookeries, yet individuals from different rookeries mix at foraging grounds. Rookeries may be impacted by processes at foraging grounds, hence rookery contributions to mixed foraging assemblages must be considered. Bimini, Bahamas, is an important foraging ground for juvenile green turtles, but rookery contributions to this assemblage have never been resolved. We generated mitochondrial DNA (mtDNA) sequences for 96 green turtles from Bimini and used Mixed Stock Analysis (MSA) to determine rookery contributions to this foraging assemblage using high-resolution (~817 base pair) and low-resolution (~490 base pair) rookery baseline data. The high-resolution data indicated that Quintana Roo, Mexico and Central Eastern Florida contributed most to Bimini. The low-resolution data indicated that Southwest Cuba and Central Eastern Florida contributed the most to Bimini. The results of the low-resolution MSA differ from a previous study conducted in Great Inagua, Bahamas which may reflect rookery size, rookery proximity to foraging grounds, the influence of currents, or a combination of these factors. While the presence of large credible intervals in our results does not permit explicit interpretation of individual MU contributions identified in MSAs, our results reveal substantial relative differences in rookery contributions to Bahamian foraging assemblages. Our study highlights the importance of regularly monitoring rookery contributions, resolving regional recruitment patterns to inform conservation, and the importance of using high resolution data in future MSA’s to improve rookery contribution accuracy.