The biodiversity and the quality of subterranean waters have been comparatively studied in the Haouz plain near Marrakesh and in the Tafilalet, in south-eastern Morocco. For this purpose, physicochemical and faunistic analyses were carried out on the water of ten wells and springs located in the area of Marrakesh, and in Errachidia area respectively. In the wells of Marrakesh, the average stygobiologic diversity is relatively high in the wells located upstream the dumping from the city where the ground water presents low contents of nitrates and orthophosphates. In contrast, the wells located in the spreading zone of Marrakesh wastewaters are characterized by the scarcity or the absence of stygobitic species; in these latter wells, the water is highly polluted. It is rich in nitrates, nitrites, ammonium, and the conductivity is rather high. In the area of Errachidia the faunistic inventory gathers some ten species, some of which are living in hot springs. The subterranean water is highly mineralised. In the two studied areas, the biodiversity decreases when well water is locally polluted, and the subterranean fauna completely disappears if the degree of contamination is important. This relation between the biodiversity and water quality which had already appeared in surface water, is confirmed within the wells of Marrakech. The groundwater fauna of both two areas presents similarities in relation to their geological history, mainly the various marine cycles of marine transgressions-regressions, which were at the origin of the settlement of the ancestors of the extant species, and the Atlasic orogenesis which separated the common ancestral populations into two separated stocks, involving a different evolution of the ancestors and a resulting speciation by vicariance.