Human-made structures are increasingly found in marine coastal habitats. The aim of the present study was to explore whether urban coastal structures can affect the genetic variation of hard-bottom species. We conducted a population genetic analysis on the limpet Patella caerulea sampled in both natural and artificial habitats along the Adriatic coast. Five microsatellite loci were used to test for differences in genetic diversity and structure among samples. Three microsatellite loci showed strong Hardy-Weinberg disequilibrium likely linked with the presence of null alleles. Genetic diversity was significantly higher in natural habitat than in artificial habitat. A weak but significant differentiation over all limpet samples was observed, but not related to the type of habitat. While the exact causes of the differences in genetic diversity deserve further investigation, these results clearly point that the expansion of urban structures can lead to genetic diversity loss at regional scales.