AbstractPrey preferences are important drivers of predator–prey interactions and trophic network structure. We present a species‐level selection analysis for the endangered Zingel asper (L. 1758) and its prey within the Baetis (Ephemeroptera) genus. By combining robust diet metabarcoding data with fine‐scale prey community data, we revealed that Z. asper selected four Baetis species differently, despite being largely considered as ecologically similar species. Our results suggest that fine‐resolution analysis of prey selection may be key for understanding trophic interactions and for improving the conservation and management of fish.