Several studies report the high capacity of bioindication of Isopoda (Crustacea, Oniscidea), related to their important ability to accumulate contaminants, useful in soil ecotoxicology and in bioindication activities. Any change in the Isopods population, diversity, and life cycle can indicate relevant pollution levels. The analysis of target tissues, as hepatopancreas, is another emerging approach (from a cytologic/histologic level) to detect contaminant accumulation from different sources. In this study, tissue disaggregation procedures were optimised on hepatopancreas, and Flow Cytometry (FC) was applied to detect cell viability and several cell functions. After disaggregation, two hepatopancreatic cell types, Small (S) and Big (B), were still recognizable: they differ in morphology and behaviour. The analyses were conducted for the first time on Isopods from sites at different conditions of ecological disturbance through a cytometric re-interpretation of ecological-environmental parameters. Significant differences in cell functional parameters were found, highlighting that Isopod hepatopancreatic cells can be efficiently analysed by FC and represent standardisable, early biologic indicators, tracing environmental-induced stress through cytologic/histologic analyses.