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Coastal lagoons are semi-isolated ecosystemsexposed to wide fluctuations of environmental conditionsand showing habitat fragmentation. These features mayplay an important role in separating species into differentpopulations, even at small spatial scales. In this study, weevaluate the concordance between mitochondrial (previouspublished data) and nuclear data analyzing the geneticvariability of Pomatoschistus marmoratus in five localities,inside and outside the Mar Menor coastal lagoon (SESpain) using eight microsatellites. High genetic diversityand similar levels of allele richness were observed acrossall loci and localities, although significant genic andgenotypic differentiation was found between populationsinside and outside the lagoon. In contrast to the FST valuesobtained from previous mitochondrial DNA analyses(control region), the microsatellite data exhibited significantdifferentiation among samples inside the Mar Menorand between lagoonal and marine samples. This patternwas corroborated using Cavalli-Sforza genetic distances.The habitat fragmentation inside the coastal lagoon andamong lagoon and marine localities could be acting as abarrier to gene flow and contributing to the observedgenetic structure. Our results from generalized additivemodels point a significant link between extreme lagoonalenvironmental conditions (mainly maximum salinity) andP. marmoratus genetic composition. Thereby, these environmentalfeatures could be also acting on genetic structureof coastal lagoon populations of P. marmoratus favoringtheir genetic divergence. The mating strategy of P. marmoratuscould be also influencing our results obtained frommitochondrial and nuclear DNA. Therefore, a specialconsideration must be done in the selection of the DNAmarkers depending on the reproductive strategy of thespecies

Environmental variables, habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus