The feeding ecology of 2 sympatric mysid species within the food web of the St. Lawrence Middle Estuary was studied to determine their trophic position and potential mechanisms of coexistence. These abundant predators were clearly distinguished by differences in foraging behaviour. In feeding experiments involving multi-prey assemblages, predation and ingestion rates of Mysis stenolepis were greater than for Neomysis americana, except for small prey. M. stenolepis showed highest predation rates on and preference for Eurytemora affinis nauplii and copepodites, and did not feed on the most abundant prey, the veliger stage of the zebra mussel Dreissena polymorpha. In contrast, N. americana showed highest predation rates on and preference for small prey species such as rotifers, nauplii and veligers. When densities of preferred prey declined in the second half of the experiment, both mysid species showed a shift in predation towards the less preferred prey. M. stenolepis switched to filter feeding, with higher predation rates on veligers, whereas N. americana increased predation on small E. affinis copepodites. Stable isotope analysis and feeding experiments suggested 3 trophic levels in the food web, with a high degree of omnivory. The δ 13 C values for the 2 mysid species were similar and supported by the same carbon source, mostly of autochthonous origin. However, their δ 15 N differed significantly by 2.2 ‰, indicating that the composition of their diet differed in terms of ingested and assimilated food items. These results suggest that co-existence of the sympatric mysid populations is achieved by reduced competition due to foodniche partitioning. Flexibility in their foraging behaviour allowed mysids to exploit multiple prey groups that undergo temporal and spatial fluctuations in the highly dynamic estuarine transition zone of the St. Lawrence Middle Estuary.