According to ecological theory two species cannot occupy the same niche. We tested the extent to which two sympatric deposit-feeding amphipods, Monoporeia affinis and Pontoporeia femorata, partition trophic resources by applying nitrogen isotope analyses (δ15N) of amino acids. We found that trophic position (TP), and resynthesis index (∑V; a proxy for degradation status of ingested material prior to assimilation by the consumer) differ between species. The surface-feeding M. affinis had higher TP and intermediate ∑V; both pointing to a large contribution of metazoans in its diet. P. femorata, which feeds in the sub-surface layers, had lower TP and a bimodal distribution of the ∑V values, supporting previous experimental evidence of a larger feeding niche. We also evaluated whether TP and ∑V values have consequences for amphipod fecundity and embryo viability and found that embryo viability in M. affinis was negatively linked to TP. Our results indicate that the amino acid-δ15N data paired with information about reproductive status are useful for detecting differences in the trophic ecology of sympatric amphipods. Key words: Compound-specific stable nitrogen isotope analyses, amino acids, trophic level, resynthesis index, reproductive status, Baltic Sea.