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This study analyses the allozymic variation of 20 presumptive loci in eight populations of Rana saharica from Morocco. Populations were collected from the very different climatic zones of this country: the Rif area, the Atlas mountains and the desert. Moroccan water-frog populations are genetically well differentiated from the geographically closed Algerian populations. Thus, to check if such a differentiation process is taking place within Moroccan water frogs, we attempted to analyse the genetic structure and patterns of gene flow of Moroccan populations, by means of estimates of Hardy-Weinberg equilibrium, F-statistics and indirect measures of gene flow. F-ST (0.250) and F-IS (0.254) values were similar, which means that both intra and interpopulation differentiation contribute equally to the amount of genetic divergence revealed. F-IS values indicated some degree of structure within ponds, which is possibly related to the homing behaviour of some amphibians. On the other hand, F-ST and genetic distances between populations were not very high. Despite the low levels of gene dow estimated, together with the homing behaviour revealed and the spatially discontinuous distribution, it was found that genetic differentiation among populations was not as high as expected. The likelihood of genetic homogeneity being the consequence of continuous population extinction and recolonization events is discussed.