Abstract Background, Aims, and Scope The springtail Folsomia candida is a commonly used model species in ecotoxicological soil testing. The species reproduces parthenogenetically and, thus, laboratories use different clonal lineages. In this study, we investigated if genetic divergence between F. candida strains impacts the reaction to chemical stress and may thus affect the outcome of toxicity tests. Methods In two exposure assays (life-cycle reproduction test and avoidance behaviour test), three laboratory strains of F. candida from Portugal (PTG), Spain (SPN) and Denmark (DNK) were exposed to different concentrations of the reference chemical phenmedipham. Genetic divergence among strains was estimated based on mitochondrial COI sequence data. Results No significant differences between tolerance towards phenmedipham exposure were observed in a reproduction test. In contrast, one strain (SPN) showed a decreased susceptibility to phenmedipham compared to the other strains (PTG and DNK) in the avoidance assay. Discussion A phylogenetic tree based on mitochondrial COI sequences revealed clear genetic differentiation between both ‘reaction types’. Thus, we found a potential lineage dependent stress reaction in avoidance behaviour towards the pesticide. Conclusions Our findings have implications for the comparability of test results among laboratories. Reproduction tests seem to be more robust towards interclonal genetic differentiation than avoidance tests. Recommendations and Perspectives We recommend the use of molecular tools for simple and cost effective genetic characterization of F. candida strains used in chemical avoidance tests. Closer investigations concerning the relation between genetic relatedness and chemical response will provide a more detailed and comprehensive picture on the role of intraspecific genetic differentiation in stress tolerance.