The present study checks on the validity of the hypothesis that heterozygosity and the fluctuating asymmetry (FA), common measure of the developmental stability, are linked in populations of wild and cultured stocks of Sparus aurata from five countries. Muscle and liver samples were analysed for variation in 26 allozymes and three microsatellite loci. Pectoral fin rays and upper and lower gill rakers of the first branchial arch were counted on the left and on the right sides of each fish. Fluctuating asymmetry existed in the majority of the samples although their values were consistently low, (0·305±0·147), but higher in the cultured samples. The allozyme heterozygosity values were always high, but lower in the cultured samples. The microsatellite DNA analysis produced similar results. Heterozygosity was higher in cultured individuals (except for the Greek samples). These findings seem to be early evidence that the reared samples are losing some genetic variation, especially due to the loss of the rarest alleles (which were present in the wild populations). Genetic drift, probably caused by propagation practices, is most likely responsible for the decrease of the genetic variation. No distinct pattern of geographic separation was identified.