Aphanius fasciatus (Valenciennes, 1821) is a small cyprinodontid fish with external sexual dimorphism. Endemic to the Mediterranean. It is strongly eurythermic and euryhaline. This study concerns morphological differences and genetic structure of this species in North Africa, the most westerly area of its distribution range. A total of 141 individuals were collected using a beach seine from three locations in Algeria: Mellah lagoon (N = 41) and its neighbour Marsh (N = 30), Ayata Lake (N = 29) and one in Tunisia: Bizerte lagoon (N = 41). For morphometric analysis, 13 landmarks were positioned on lateral photographs taken of the fish. Shape information was extracted from the data with a procrustes superimposition and grouped by gender and location. Proteins extracts were obtained from liver and muscle and used for allozymic analysis to determine genetic variations across locations. Seven isoenzymatic systems: MDH (malate dehydrogenase), GOT (Glutamate oxaloacetate transaminase), PGI (phosphoglucose isomerase), PGM (phosphoglucomutase), EST (esterase), IDH (isocitrate dehydrogenase), LDH (lactate dehydrogenase) were revealed using enzyme-specific stains. Canonical variate analysis and discriminant function among procruste covariation matrix shows that the shape of the specimen of Ayata Lake is different from those of the three other localities. Ayata Lake fishes have heads shorter than the other populations; their anal fin is smaller and its distance from pelvic fin is more important than observed in other populations. Genetically, Ayata Lake population is distinguished from other localities by the highest values of Fst (fixation index), Ap (private alleles), Ar (Allelic richness). The Jackknife test shows that the PGM system is responsible of this variation. Evolution and adaptation mechanisms of this species according to different habitats are discussed.