The patterns of genetic differentiation and levels of genetic diversity among striped dolphin (Stenella coeruleoalba) populations from the North Atlantic Ocean (N=45 individuals) and the central and western Mediterranean Sea (N=78) were investigated using five polymorphic microsatellite loci. A North Pacific sample (N=14) was added as an out-group. Two of the markers were tetranucleotide repeats tested for the first time in this species. The Mediterranean, Atlantic and Pacific samples displayed a mean number of alleles per locus of 11.2, 13.4, and 9.6 respectively, suggesting a high but variable polymorphism across loci. The Mediterranean sample displayed particular characteristics: (i) the lowest allelic richness and expected heterozygosity (HeMediterranean=0.76, while HeAtlantic=0.83 and HePacific=0.85); (ii) a significant departure from Hardy–Weinberg equilibrium (P<0.001; FIS=0.050); and (iii) a significant linkage disequilibrium between two pairs of loci. These last two features, present neither in the Atlantic sample nor in the Pacific one, suggest that the western Mediterranean population might possibly be further subdivided. Significant genetic differentiation was detected between the Mediterranean and Pacific populations, and between the Mediterranean and Atlantic populations. However, pairwise Wright's FST was not significantly different from zero between the two geographically isolated Atlantic and Pacific populations.