A new approach to mixed stock analysis that informs on the management and conservation of hawksbill in the wider Caribbean: the case of the legal fishery in Jardines del Rey, Cuba, International Journal of Marine Science, 7(33): 316-343 (doi: 10.5376/ijms.2017.07.0033) Abstract Researchers have used mixed stock analysis (MSA) to infer the relevance of rookeries in sea turtle aggregations for conservation/management purposes. However, their approaches and assumptions are not always homogeneous or realistic. We assayed new MSAs using the annual haplotype frequencies of aggregations and rookeries of Eretmochelys imbricata in the Wider Caribbean (WC), and the population size was selected according to the sampler year most relevant on the maturity of the aggregation. The MSA results obtained using this approach were compared with MSAs executed with grouped haplotype frequency data as has been the most common practice in the literature. The relationship of Jardines del Rey (JR) legal fishing aggregation (Cuba) to other aggregations and rookeries in the region was analyzed with data collected in 2004 to 2006 and during the 1990s. The JR non-adult fishing ground presented high genetic diversity and Mexican rookery was identified as the primary contributor using haplotypes at the 384 bp length and each MSA approach that was used, congruent with the demographic growth reported for this rookery. Using haplotypes at the 740 bp length, the primary contributor to non-adult turtles at JR differed according to the MSA approach used, alternating between Mona Island and the Mexican rookery. Jardines del Rey is a route usually taken by non-adult hawksbills of diverse origin, reflecting the need to strengthen the sampling and conservation efforts on the WC rookeries with rare or orphan haplotypes, and to warn about the impact of the fishery occurring in similar areas. Likewise, adult turtles from JR were highly diverse and from multiple origins, with this area serving as a migratory corridor for first breeders (females) to many WC breeding grounds. Caution should be employed in any MSA approach due to the influence effect of sequence length, selection of the rookery size and haplotype frequencies, as well as other assumptions that may affect the estimated contributions.