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Cryptic species are rarely considered in ecotoxicology, resulting in misleading outcomes when using a single morphospecies that encompasses multiple cryptic species. This oversight contributes to the lack of reproducibility in ecotoxicological experiments and promotes unreliable extrapolations. The important question of ecological differentiation and the sensitivity of cryptic species is rarely tackled, resulting in a substantial knowledge gap of the vulnerability of individual cryptic species within a species complex. In times of agricultural intensification and the frequent use of pesticides, there is an urgent need for a better understanding of the vulnerability of species complexes and possible differences in adaptive processes. We used the cryptic species complex of the aquatic amphipod Gammarus roeselii, which comprises at least 13 genetic lineages and spans from small-scale endemic lineages in Greece to large-scale distributed lineages in central Europe. We exposed eleven populations belonging to four genetic lineages to the neonicotinoid thiacloprid in an acute toxicity assay. We recorded various environmental variables in each habitat to assess the potential pre-exposure of the populations to contaminants. Our results showed that the populations differed up to 4-fold in their tolerances. The lineage identity had a rather minor influence, suggesting that especially recent pre-exposure to the substance (or similar substances) triggered adaptive mechanisms. The extent to which these mechanisms are equally triggered in all lineages needs to be addressed in the future. Our study provides strong evidence that selection operates at the population …