Mortality at early life stages of fishes is widespread in nature and can be shaped by stochastic and selective processes. Selective mortality has rarely been assessed in natural conditions but now can be addressed genome-wide by studying different life stages that connect to fitness in different localities, identifying parallel evolutionary processes. Here we investigate selective mortality between settlers and six-month survivors by genotype-phenotype/environmental association studies in the sharpsnout seabream along a geographic gradient. Despite environmental conditions differ between localities, we found common signals such as lower survival for individuals hatching earlier and multiple loci with significant association to phenotypic and environmental variables such as hatch date, pelagic larval growth rate and sea surface temperature at settlement. All these parallel associations between loci and early-life traits suggest a genetic basis of early survival. Importantly, the il20rb gene shows parallel frequency changes in non-synonymous mutations in the three studied populations that may be key for selective mortality and their polymorphism maintained by antagonistic pleiotropy.