The southern Alboran Sea is a dynamic ecosystem and is highly influenced by Atlantic waters. Unfortunately, despite the importance of the mesozooplankton in this ecosystem, the number of studies on this ecosystem is low. The composition and abundance of mesozooplankton communities were studied during the summer season (July 2017) along the Moroccan Mediterranean coast between M’diq and Saïdia. A total of 14 mesozooplankton groups were identified and were dominated by copepods (48%) and cladocerans (35%). Abundance and biomass spatial distribution distinguished two main regions east and west of Al Hoceima. The same distribution pattern was observed when using copepod and cladoceran abundance. Environmental parameters (temperature, salinity, and nutrients) differed in these two regions. Our results confirm the hypothesis that the water flux from the Atlantic Ocean is responsible for the eastward gradients of the mesozooplankton abundance and diversity. Copepods were the most diversified group with 27 species, dominated by Paracalanus parvus (30.5%), Temora stylifera (14%), and Oncaea venusta (12.4%). The diversity index (H’) of copepods varied between 1.35 and 2.8 bits ind−1, and the regularity index (J) varied between 0.21 and 0.45, without a remarkable longitudinal gradient. Multivariate analysis showed that the mesozooplankton biomass, abundance, and distribution were influenced mainly by hydrology (gyres), by temperature and salinity, and to a lesser degree by phytoplankton.