The commercial comber Serranus cabrilla is widely distributed in the Atlanto-Mediterranean region, inhabiting a great variety of habitats and depths. We developed primers for 12 polymorphic microsatellite loci to analyse the genetic structure between comber populations and between their colour morphs in order to establish correct fisheries management. Characterization of 25 individuals from Columbretes Islands (Spain) showed an average large number of alleles (9.5 ± 1.3) and observed heterozygosity (0.657 ± 0.06). Only two loci showed significant departure from Hardy–Weinberg equilibrium. We found no evidence of linkage disequilibrium between pairs of loci. We rejected for primer design one clone with a microsatellite within the transposable element TX_FR2.