The identification of loci under selection (out- liers) is a major challenge in evolutionary biology, being critical to comprehend evolutionary processes leading to population differentiation and speciation, and for conser- vation purposes, also in light of recent climate change. However, detection of selected loci can be difficult when populations are weakly differentiated. This is the case of marine fish populations, often characterized by high levels of gene flow and connectivity, and particularly of fish living in the Antarctic marine environment, characterized by a complex and strong circulating system promoting individual dispersal all around the continent. With the final aim of identifying outlier loci putatively under selection in the Chionodraco genus, we used 21 microsatellites, including both genomic (Type II) and EST-linked loci (Type I), to investigate the genetic differentiation among the three recently derived Chionodraco species that are endemic to the freezing Antarctic waters. Neutrality tests were applied in interspecific comparisons in order to identify candidate loci showing high levels of genetic dif- ferentiation, which might reveal imprints of past selection. Three outlier loci were identified, detecting a higher dif- ferentiation between species than did neutral loci. Outliers showed sequence similarity to a calmodulin gene, to an antifreeze glycoprotein/trypsinogen-like protease gene and to nonannotated fish mRNAs. Selective pressures acting on outlier loci identified in this study might reflect past evo- lutionary processes, which led to species divergence and local adaptation in the Chionodraco genus. Used loci will provide a valuable tool for future population genetic studies in Antarctic notothenioids.