Previous surveys of population structure in the Atlantic-Mediterranean anchovy Engraulis encrasicolus L. have reported heterogeneity in morphology, allozyme frequencies, and mitochondrial-DNA haplotype frequencies at a regional scale. In particular, two stocks of anchovy have been detected in the Adriatic Sea. Here I review the available data with the aim to relate genetic variation with geography at the widest possible geographical scale, for investigating the evolutionary mechanisms underlying stock structure in anchovy. Correspondence analysis of allozyme frequencies (24 samples, 3 polymorphic loci) compiled from the literature indicated three distinct entities in the Mediterranean Sea. Open-sea or oceanic anchovy populations are genetically different from inshore-water populations within a region (Nei’s ^GST=0.035-0.067), while broadscale geographical variation is weak for each of these two habitat-specific forms (^GST =0.005-0.006). Mitochondrial-DNA haplotype frequencies also support the distinction between an inshore form and an oceanic form (^GST =0.067-0.107), with virtually no genetic differences among oceanic populations across the Gulf of Biscay, the Western Mediterranean and the Ionian Sea (^GST =-0.001). If natural selection on marker loci is unimportant, these results indicate the occurrence of two parapatric, genetically distinct, habitat-specific forms that are widely distributed throughout the Mediterranean Sea. Persistent allele- and haplotype-frequency differences between these forms indicates reproductive isolation and the presence of an E. encrasicolus species complex in the Mediterranean.