Several morphological and molecular studies support the north African origin of the brown snail Cornu aspersum aspersum (Müller, 1774) and evidence suggests the presence of two morphologically and genetically different haplogroups in this area. However, all investigations were confined mainly to the western Mediterranean region, whereas the genetic structure and geographical distribution of eastern Mediterranean populations remained largely unknown. The present study attempted to elucidate the fine-scale phylogeography of C. a. aspersum along the Croatian coast and islands. Both Bayesian phylogenetic inference and network-based approaches showed a strong genetic splitting of Croatian 16S rRNA, COI and cyt b sequences into two well-defined groups consistent with previous eastern and western lineages. The eastern haplotypes were more frequent and distributed over a wider geographic area than western haplotypes. The genetic admixture of eastern and western gene pools observed in three Croatian populations would signify a new secondary contact zone in Croatia between both previously defined lineages. Our results suggest that: 1) the eastern lineage, which disappeared in most Mediterranean regions, persisted in the Adriatic area probably through several climatic cycles accumulating genetic differences and 2) two or, more likely, several independent post-glaciation colonization routes crossed at this contact zone, bringing two distinct C. a. aspersum haplogroups together.