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The queen conch, Aliger gigas is a large marine gastropod mollusc that inhabits shallow seagrass meadows and sandplain habitats throughout the Caribbean. Owing to overfishing and degradation of the environment, it has become an endangered species in most of its habitat. Research on Cuban populations of A. gigas is scarce and mostly focused on conch exploitation. The present study assesses, for the first time, the genetic diversity and population structure of A. gigas from six locations on the Cuban platform, using five microsatellite loci. At most of the sampled locations, the observed heterozygosity was lower than expected and the F IS value was significantly positive, both of which suggest inbreeding. Also, we found evidence of bottlenecks for two of the locations with a deficit of heterozygotes. Although statistically significant, only 1.66% of the total variance was explained by genetic differentiation among populations, and discriminant analysis of principal components showed different degrees of overlapping between all locations. Accordingly, the results showed that there is an extensive and symmetrical exchange of genetic information. Sparse non-negative matrix factorization analysis determined the existence of three ancestral populations admixed across the sampled locations. Thus, our results suggest that A. gigas from the Cuban island platform could be a unique population, which is relevant for management and conservation strategies. [ABSTRACT FROM AUTHOR]