The Atlantic Bluefin tuna (BFT, Thunnus thynnus), one of the largest top-predator fish inhabiting the pelagic ecosystems of the North Atlantic Ocean and Mediterranean Sea, has been extensively overexploited in recent decades. However, in the Mediterranean Sea, the mixing rates between the eastern, central and western basins have not yet been fully and finally resolved. To date electronic tagging, otolith and genetic markers cannot still disentangle the pattern of tuna movements and population structuring in the basin, essential background for a proper management of BFT fisheries. Here, we used Expressed Sequence Tag-linked (EST-linked) microsatellites to explore population dynamics and adaptive evolution of Mediterranean T. thynnus. For this purpose, 16 EST-linked microsatellites were genotyped in 177 tuna individuals from the Mediterranean Sea and several methods were used to explore population genetic structuring and estimate/detect signals of local adaptation. Bayesian clustering results indicated the presence of a single cluster, corroborated also by the Correspondence Analysis and pairwise Fsrs. Similarly, the two methods used for the detection of outlier loci (LOSITAN and BayeScan), did not reveal any pattern suggesting the presence of selective pressure on the EST Simple Sequence Repeat (SSR) used. Our results suggest that the low level of polymorphism detected in this study could be ascribed to the presence of relatively conserved regions flanking these microsatellites. These genomic regions are probably not involved in physiological responses to local adaptation. (C) 2017 Elsevier B.V. All rights reserved.