The physiological adaptations of diatoms to cope with Cu limitation are largely unknown. In the present study we investigated the response to Cu limitation in two strains of the model open ocean diatom T. oceanica (CCMP 1003 and CCMP 1005), focusing on physiological and proteomic changes in the photosynthetic apparatus. Our results show remarkable differences between the adaptations of TO05 and TO03 to low Cu, highlighting significant intra specific variations.