In Croatia, wild rabbits (Oryctolagus cuniculus) are present in several East Adriatic islands, while their origin is not known (documented). To characterize their maternal origin, we have analysed partial mitochondrial DNA control region (CR-mtDNA) sequence (317-bp) in 36 wild rabbits sampled in three Croatian islands (11 in Dolin, 10 in Dugi otok and 15 in Trstenik). After comparison with other worldwide distributed wild and domestic rabbit sequences (208), two distinguished haplotypes (H1 and H2) were found in Croatian rabbits. H1 was equal to the reference rabbit sequence (GenBank accession number NC_001913) that is the most frequent haplotype present in wild and domestic rabbits and belongs to the lineage B. H2 haplotype, present in the one rabbit from Dugi otok, was just one mutation, transversion T→C at 15803, remote from the H1. The results presented in this study show extremely low CR-mtDNA diversity of Croatian rabbits and indicate their feral origin.