Among all contaminants present in the aquatic ecosystems, endocrine-disrupting chemicals (EDCs) are currently a great concern because of their high potential induction of alterations in reproductive function and consequently population dynamics. Their mode of action and associated effects on hormonal regulation have been intensively studied for fish, resulting in robust, specific and reliable biomarkers for risk assessment. Meanwhile, similar tools are lacking for invertebrates, especially crustaceans, while they are major biocenose components, playing key role in ecosystemic processes. While disruption of endocrine regulation is documented in-situ, causality between these adverse effects and their cause can not be established due to the lack of knowledge on sexual chemistry for these models. The recent trends in high-throughput proteomics allow large-scale characterization of the whole proteome of model organisms. We started to document the reproductive proteome of the freshwater amphipod, Gammarus fossarum, an ecotoxicology relevant species. For this, we used the most advanced approaches in shotgun proteomics for an extensive comparison of the female and male reproductive tissues of G. fossarum. Tandem mass spectrometry analysis of a large pool of peptides arising from trypsin digestion of both tissues was done with a high resolution LTQ-Orbitrap XL hybrid mass spectrometer (ThermoFisher). A total of 1,336 proteins were identified with high confidence and quantified using the spectral count approach. The cross-comparison of the relative abundance of these proteins in both tissues has shown that 66 and 103 proteins were preferentially expressed in the female and the male reproductive tissues, respectively. Functional annotation by PSI-BLAST searches resulted quite scarce as reproductive proteins evolve more rapidly than others genes products due to sexual selection. As gammarids reproductive biology is well described, proteins modulation throughout the reproductive cycle is currently assessed for empirical functional annotation. Our study should result in interesting biomarkers for freshwater biomonitoring based on the G. fossarum sentinel.