Allozyme variation was used to investigate for the first time the genetic structure of European anchovies, Engraulis encrasicolus (Linnaeus, 1758), along the Moroccan coasts. A total of 420 individuals were collected at 11 sites during the anchovy spawning period of 2012. Eleven loci were tested, among them only LDH* [E.C:1.1.27] and PGM * [E.C:5.4.2.1] were polymorphic. Statistical analysis results showed no significant differentiation between samples (overall FST = 0.0077, p = 0.13). Genotypic proportions were not in accordance with Hardy-Weinberg predictions; an important heterozygote deficiency was detected (FIS = 0.48959 ± 0.07863, p < 0.001). The results are compared with those of other studies and are discussed in relation to hydroclimatic factors in the Moroccan coasts and to species behaviour in such environment.