Two anchovy forms identified from their external morphology and designated as 'Silver' and 'Blue' anchovies were captured in Mersin Bay (Eastern Mediterranean Sea). Silver anchovy seemed to inhabit shallower waters (9-77 m) than Blue anchovy (majority at depths of 69-111 m). Significant differences in body shape, which was analyzed through geometric morphometrics, and in otolith shape, examined using Fourier analysis, separated the two forms. Length polymorphisms at two intron and 9 microsatellite loci showed strong genetic differences between the two forms. Mersin-Bay Blue anchovy were genetically related to Engraulis encrasicolus from the Western Mediterranean Sea. Mersin-Bay Silver anchovy possessed an original genetic composition that distinguished them from both E. encrasicolus and Engraulis albidus at the two intron loci, while presenting affinities to E. albidus based on microsatellite markers. Mersin-Bay Silver anchovy were assigned to the latter species, of which they are considered as a geographically isolated population. This is the first record of E. albidus in the Levantine basin and confirmation of its presence in the Eastern Mediterranean Sea. These results have implications for the management of anchovy populations and their habitats. (C) 2014 Elsevier B.V. All rights reserved.