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Allozyme electrophoresis and morphometric analyses were used to investigate the stock structure of European anchovies (Engraulis encrasicolus L.) captured by Italian vessels in the Adriatic Sea. Twenty four putative enzyme loci were studied, all of which exhibited genotypic proportions in accordance with Hardy-Weinberg predictions. Two loci, IDHP-2 * (isocitrate dehydrogenase, 1.1.1.42) and G3PDH-2 * (glycerol-3-phosphate dehydrogenase, 1.1.1.8), showed significant allele-frequency differences among samples. IDHP-2 * 100 frequencies ranged between 0.35 and 0.88, with lower frequencies recorded in northern waters and areas close to the Italian coastline, while G3PDH-2 * 100 frequencies followed a similar, if less distinct, pattern. For both loci, the trends observed were spatially stable over a 2 yr sampling period. A putative stock-boundary was superimposed onto a map of IDHP-2 * 100 frequencies, and a bootstrapped dendrogram confirmed the genetic separation of the two putative stocks, one located around the north-western Adriatic and the other in the central-southern region. Canonical variate analysis (CVA) of morphometric data collected using a “truss network” indicated that the two putative stocks were morphologically distinct; 89.6 and 88.3% of north-western and central-southern anchovies, respectively, were correctly assigned by discriminant-function analysis. This variation may be related to the presence of two anchovy colour phenotypes, silver and blue, in the Adriatic Sea. Silver anchovies are characteristic of northern areas, while the larger blue fish are found mainly in the deeper southern waters. Current assessment models for the fishery are based on the concept of a consistent identity between consecutive catches at single ports, which our data reject. We discuss the possibility of partitioning fishing effort based on the proportions of the two stocks landed at individual ports.