The calanoid copepod Eurytemora affinis is a cryptic species complex composed of 6 genetically distinct but morphologically similar clades. These dominate planktonic communities, and are considered the keystone species of many estuarine food webs in the northern hemisphere, channeling carbon and energy to higher trophic levels. In doing so, they directly influence the recruitment of many fish species. The Atlantic and the North-Atlantic clades co-occur in the St. Lawrence estuarine transition zone (Québec, Canada), but their distribution is spatially segregated. Both clades exploit various habitats depending on their physiological tolerance to salinity and resource availability favouring niche partitioning. In this review, we discuss recent studies on E. affinis, focussing on distribution patterns, and the ecological and genetic differentiation of co-occurring clades. The aim is to provide a clearer understanding of the influence of this species complex on productivity and ecosystem functioning in the St. Lawrence estuarine transition zone, which is an important fish nursery.