The portunid crab Liocarcinus depurator is the dominant decapod crustacean present on mud bottoms of the continental shelf of the Mediterranean Sea. In order to better describe its genetic structure, a total of 11 microsatellites were isolated and tested in 28 L. depurator individuals from the Mediterranean locality of Tarragona. Initially, microsatellite isolation was carried out using the FIASCO methodology, but only 2 useful primer pairs could be designed. Given the low yield obtained, an alternative method based on 454 next-generation sequencing was assayed, which provided excellent results and from which another 9 primer pairs gave positive genotyping. All loci tested were polymorphic, and 2 to 24 (mean 10.54) alleles per locus were identified. The observed and expected heterozygosities per locus ranged from 0.214 to 0.926 and from 0.232 to 0.962, respectively. One locus (Ldep10) showed the presence of null alleles according to the Brookfield estimator implemented in MICROCHECKER. Nevertheless, none of the markers deviated significantly from Hardy–Weinberg equilibrium or showed evidence of linkage disequilibrium. This set of 11 markers is being used to study the population structure and genetic diversity of Liocarcinus depurator populations from both Mediterranean and adjacent Atlantic waters.The portunid crab Liocarcinus depurator is the dominant decapod crustacean present on mud bottoms of the continental shelf of the Mediterranean Sea. In order to better describe its genetic structure, a total of 11 microsatellites were isolated and tested in 28 L. depurator individuals from the Mediterranean locality of Tarragona. Initially, microsatellite isolation was carried out using the FIASCO methodology, but only 2 useful primer pairs could be designed. Given the low yield obtained, an alternative method based on 454 next-generation sequencing was assayed, which provided excellent results and from which another 9 primer pairs gave positive genotyping. All loci tested were polymorphic, and 2 to 24 (mean 10.54) alleles per locus were identified. The observed and expected heterozygosities per locus ranged from 0.214 to 0.926 and from 0.232 to 0.962, respectively. One locus (Ldep10) showed the presence of null alleles according to the Brookfield estimator implemented in MICROCHECKER. Nevertheless, none of the markers deviated significantly from Hardy–Weinberg equilibrium or showed evidence of linkage disequilibrium. This set of 11 markers is being used to study the population structure and genetic diversity of Liocarcinus depurator populations from both Mediterranean and adjacent Atlantic waters.