Somatic morphology and otolith shape were used to discriminate four samples of Atherina boyeri from three different habitats: Mellah lagoon (n = 269), Annaba Gulf (144 punctuated and 194 unpunctuated individuals) and Ziama inlet (n = 147) in eastern Algeria. For each individual, somatic morphology was described with 13 metrics and eight meristic measurements, while the otolith contour shape of 452 individuals from the three habitats was analysed using Fourier analysis. Then, two discriminant analyses, one using the 13 metric measurements and the other using Fourier descriptors, were used in order to discriminate populations of A. boyeri. The results of the discriminant analyses based on the two methods were similar, and showed that this species could be discriminated into three distinct groups: (1) marine punctuated, (2) lagoon and marine unpunctuated and (3) estuarine. These results are consolidated by the comparison of the Mayr, Linsley and Usinger coefficient of difference for the meristic parameters according to the location origin, where the difference reached a racial or even sub-specific level for some characters, depending on which pairs of populations were compared.