Allozyme analysis on 20 putative enzyme-coding loci and RAPD analysis on 154 markers, amplified by eight decamer random primers, were used to assess the genetic variation of striped red mullet, Mullus surmuletus L., collected from six locations in the Mediterranean Sea. Both methods were able to detect a high degree of genetic polymorphism. For both methods, estimates of variance of allele frequencies (FST), and chi2 analyses, revealed significant differences (P < 0.05) among samples. Nei's genetic distance (D) among samples was low (mean D=0.011 for allozymes; mean D=0.018 for RAPDs) with data from both approaches revealing the sample from France to be most distinct from the Greek samples. Nevertheless, although most of the genetic variation in allozymes was not correlated with geographical distance, a correlation between genetic affinities and geographical area was found with RAPDs. It seems therefore that the RAPD method showed a more pronounced effect of isolation-by-distance in comparison with allozymes, probably because of the different number of markers of the red mullet genome examined with each method. Overall, the RAPD technique can be introduced as a complementary tool in the population genetics of marine fishes, providing supplementary information in their genetic stock structure analysis.