Melloulou River, which is located in Middle Atlas of Morocco, is a good example of a very wet and poorly known basin, and therefore of special conservation concern. The aim of this study was to draw up an initial inventory of the benthic macroinvertebrates taxa, and to analyze its longitudinal distribution in the basin, particularly searching for the main abiotic factors addressing its zonation for improving future management and conservation actions. The study allowed identifying 161 taxa belonging to 127 genera and 80 families, most new records for northeast Morocco. The biotypology, which was studied by using Foucart' Factorial Correspondence Analysis (FCA), Partial Triadic analysis (PTA), and IndVal showed a longitudinal distribution of macroinvertebrates mainly governed by altitude, slope and current velocity. The studied biota revealed the presence of three assemblages and an important number of ubiquitous species not included in any group. The first group is located in the upper courses of Melloulou River representing a community proper of a crenon-rhithron zone; the second occurs in the middle and lower courses, and clearly reflects the community of a large potamon; the third one is a mixture of taxa capable to colonize the entire study area. Our finding, highlight the singular aquatic biodiversity occurring in the Melloulou River and its extraordinary changing water dynamic over time, which are key factors for future monitoring, as well as managing and conservation actions.