The limpet Nacella concinna (Strebel 1908) was the focus of numerous studies dealing with Antarctic benthos. One of the main characteristics of the species is the presence of two distinguishable morphotypes, one inhabiting the intertidal (during summer) and the other inhabiting the subtidal. For a long time these forms were considered as an expression of phenotypic plasticity, since previous studies did not found genetic differences between them. In the present work, we performed both a morphometric and a genetic differentiation analysis (using ISSR-PCR markers) of these two forms in three stations sampled at Potter Cove, South Shetland Islands. The results confirmed the morphological differences between intertidal and subtidal forms reported in other Antarctic localities. The genetic differences detected indicate that the two forms can be considered as genetically distinct populations maintaining low levels of gene flow. The degree of reproductive isolation of the ecotypes is discussed, as well as the possible origin of the divergence. The genetic differentiation observed can also have behavioral and physiological correlates, pointing out the importance of taking into account the potential differences in the response of both populations to different conditions in future studies in this species.