Objectives. Next generation sequencing and mass spectrometry technologies have recently expanded the availability of whole transcriptomes and proteomes beyond classical model organisms in molecular biology, even in absence of an annotated genome. These advancements are paving the way to explore the molecular physiology and the mechanisms of toxicity in environmentally relevant species, such as the amphipod G. fossarum. Here we present the results obtained combining systems biology and proteogenomics approaches to get functional insights in the reproductive system of G. fossarum and to identify different mechanistic effects of toxicants in the amphipod’s testes. Methods. We performed co-expression network analyses (based on the R package Weighted Gene Co-expression Network Analysis, WGCNA) on shotgun proteomics data obtained from i) male and female gonads at different maturations stages and, ii) from testes of males exposed during their spermatogenesis at different concentrations of cadmium (Cd), methoxyfenozide (MET) or pyriproxyfen (PYR). Results. We identified groups (modules) of co-expressed proteins (i.e. whose expression is highly correlated) significantly associated with biological processes, such as the secondary vitellogenesis in the female embryos, and spermatozoa morphogenesis and energy metabolism in the testes. In particular, we identified taxonomically restricted proteins that may play a central role in the oocyte maturation. Moreover, we found that different modules of testicular proteins were significantly correlated with the different contaminants we studied. These results show the interest of systems biology approaches for identifying distinct mode of action even in the presence of similar toxicological responses. Conclusion. We showed that co-expression network analysis are a powerful integrative tool to investigate the –omics data issued from a proteogenomic approach in G. fossarum and that provide functional information about many unknown proteins and mode of action of environmental contaminants