The development of renewable and low-carbon energy sources means that strategic elements such as lithium (Li) are increasingly being used. The data available on the effects of Li on aquatic organisms are relatively scarce. The copepod Eurytemora affinis, widely distributed in the brackish estuarine waters of the northern hemisphere, is a species of choice in ecotoxicology but in fact constitutes a cryptic species complex, composed of at least six cryptic species. Cryptic diversity can lead to misinterpretation and alter the reproducibility of routine ecotoxicological tests. In the present study, two cryptic species of the E. affinis complex from the Seine (European clade) and the St. Lawrence (North-Atlantic clade) estuaries were used to assess Li toxicity and to compare their differential sensitivity. Larvae were exposed to different concentrations of Li (0.4, 4.39, 35.36 and 80.83 mg L−1) under semi-static conditions for 96 h. Larval development stages were determined and log-logistic functions were fitted to evaluate mortality (LC50) and growth (EC50) parameters. After 96 h of exposure, the results showed that the European and North-Atlantic clades had LC50 values of 55.33 and 67.81 mg L−1 and EC50 values of 28.94 and 41.45 mg L−1, respectively. A moderate difference in sensitivity to Li between the European and North-Atlantic clades of the E. affinis complex was observed. Thus, the cryptic species diversity should be considered using E. affinis to avoid bias in the interpretation of the data. Despite environmental concentrations of Li are expected to increase over the next years, EC50 and LC50 found for E. affinis cryptic species are largely higher than Li environmental concentrations to provoke extreme effects.