Harpacticoids can discriminate between biofilms of different bacterial strains. We investigated whether assimilation of bacteria is selective and whether harpacticoids select for the most nutritional bacteria. We specifically focused on the role of bacterial characteristics in copepod food selection. Trophic biomarkers (stable isotopes, fatty acids) were used to test selective assimilation of three bacteria by the harpacticoids Platychelipus littoralis and Delavalia palustris, all isolated from a salt marsh. The bacteria Gramella sp., Jannaschia sp. and Photobacterium sp. with contrasting ribosomal protein and fatty acid contents were 13C-labelled and offered in a food patch choice experiment with monospecific and combination treatments (single and two strains per microcosm respectively). Low assimilation of bacterial carbon and lack of significant fatty acid transfer proved that bacteria were a poor food source for the harpacticoids. Assimilation was copepod species-specific and bacteria strain-specific (preference for Photobacterium). However, only a low degree of selective feeding occurred; it can partly be explained by bacterial extracellular metabolites rather than by biochemical content and densities. Finally, the energetic cost of differential bacterivory resulted in a negative fatty acid balance for Platychelipus, while Delavalia showed an improved fatty acid profile and thus a positive response to the low-quality bacterial food.