Although soft-bottoms are the largest ecosystem on Earth in terms of area, only a small percentage of their macrobenthos has been studied and most of its species are not yet described. Herein, the most up-to-dated comprehensive inventory and the broad-scale baseline of the soft-sediment macrozoobenthos in semi-enclosed coastal systems (SECS) of the Moroccan Atlantic and Mediterranean coasts (3500 km) is presented. In total, 496 species (7 phyla, 21 classes, 65 orders and 201 families) were recorded among which 95 species were exlusively Mediterranean, 99 species were Atlantico-Mediterranean SECS and 302 species exclusively Atlantic. The best multivariate model, explaining 33% of the total variation observed in benthic assemblages’ composition, included the type of the SECS (estuaries vs lagoons vs bay), the marine ecoregion (Atlantic vs Mediterranean), the surface of the SECS and the environmental features (minimal temperature, minimal and maximal salinity) as predictors of benthic macrofauna composition in the Moroccan SECS. In contrast to the general latitudinal diversity gradient (LDG) pattern, our results showed that species richness and taxonomic diversity showed no relationship with latitude. Such differences in benthic macrofaunal composition across a large scale could result from the fact that each ecosystem has its own specific characteristics, which implies an individualistic approach to ecosystem ecology. The sample of the 12 SECS considered in this study covers most of the range of variation along the coasts of Morocco. The current compilation is relevant in such poorly known area at the global 43 scale and fulfills a knowledge gap on benthic macrofauna in SECS of the Southern part of the North-Eastern Atlantic and Mediterranean ecoregions. However, the knowledge gained here is insufficient to address perceived shortfalls in knowledge of biodiversity, its importance to ecosystem function, and the threats and consequences of disturbance by anthropogenic activities.