Using thirteen microsatellite loci for Mullus barbatus and Mullus surmuletus collected in the Mediterranean Sea, the biogeographic boundaries, genetic distribution among and within basins and the impact of prolonged exploitation in both species were investigated as a basis for understanding their population dynamics and for improving Mullus spp. stock management. Different level of diversity indices among these co-occurring species were obtained, with M. barbatus showing higher allele richness and higher mean observed and expected heterozygosity than M. surmuletus. Reduced contemporary effective population size (Ne) and M-ratio values found in both species likely reflects recent demographic changes, due to a combination of high fishing pressures, habitat fragmentation and naturally occurring fluctuations in population size. Different patterns of genetic connectivity among populations sampled within the Mediterranean were observed for both species. Higher genetic structure was found for M. barbatus as opposed to a more homogenous pattern observed in M. surmuletus samples. Adriatic populations, previously considered panmictic and isolated from other Mediterranean regions, showed geographical partitioning within the basin but also population connectivity with the northern Ionian and Tyrrhenian Seas. Our results highlight the need for temporal sampling in understanding the complex pattern of population connectivity in the Mediterranean, particularly for management purposes.