In this study, the interactions between two semi-aquatic mammals, the endangered Pyrenean desman Galemys pyrenaicus and the Eurasian water shrew Neomys fodiens, were investigated through the analysis of their summer diet using next-generation sequencing methods, combined with analyses of prey selectivity and trophic overlap. The diet of these predators was highly diverse including 194 and 205 genera for G. pyrenaicus and N. fodiens respectively. Overall, both species exhibited rather non-selective foraging strategies as the most frequently consumed invertebrates were also the most frequent and abundant in the streams. This supported a generalist foraging behaviour for G. pyrenaicus and N. fodiens in the study area. The Pianka index (0.4) indicated a significant but moderate dietary overlap as G. pyrenaicus mostly relied on prey with aquatic stages whereas prey of N. fodiens were mainly terrestrial. Moreover, no difference in G. pyrenaicus prey consumption was found in presence or absence of N. fodiens. A differential use of trophic resources through mechanisms such as plastic feeding behaviour or differences in foraging micro-habitat are likely to facilitate the coexistence between these two mammal species.