The striped dolphin (Stenella coeruleoalba) is a small, pelagic and cosmopolitan cetacean. Though it is the most common dolphin species in the Mediterranean Sea, it is not considered resident in the Croatian part of the Adriatic Sea. Fifteen striped dolphins were found dead in the Croatian part of the Adriatic Sea in the last eight years (1999–2007). More specimens were found in southern than in the northern part of the Adriatic. Analysis of twelve microsatellite loci and sequencing of a 882 base pair (bp) fragment of the mitochondrial DNA (mtDNA) control region were performed for genetic characterization. The mean allelic diversity (7 ±0.78) and mean expected heterozygosity (0.727 ±0.05) reveal high genetic variation. Significant deviation from Hardy-Weinberg equilibrium was observed at two loci. Sequence analysis of the mtDNA control region identified seven unique haplotypes with 22 polymorphic sites in ten individuals. The haplotype diversity (0.911 ±0.077) was high, while nucleotide diversity was strikingly low (0.006 ±0.003). Results presented here support the notion of the striped dolphin not being resident species in Croatian part of the Adriatic Sea.