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Due to its crucial role in the ecosystem, phytoplankton is incorporated in marine ecosystem models. Most models however neglect the evolutionary potential of phytoplankton. Previous resurrection experiments with a spring bloom dinoflagellate suggest that the past century of global warming has caused an adaptive response in an important life cycle trait, the encystment rate. Here, based on this resurrection case study, we apply an advanced ecosystem model including selection and mutation, to test whether a temperature increase could induce a change in encystment. In line with the findings from resurrection experiments, our results show that in warmer waters strains with a lower encystment rate benefit over those with a higher encystment rate. The magnitude of change in encystment rate is however only reproduced, if additional factors, like eutrophication and a cyst mortality that increases with temperature, are considered. By using this ecosystem model including selection and mutation, we demonstrate that ecosystem modeling represents a powerful approach to investigate the adaptive potential of phytoplankton.