The functioning of natural communities is the cumulative outcome of multifaceted and intersecting ecological and evolutionary processes occurring at species level. Species are not stable entities but evolve in consequence of contingent factors including the relationships they establish with the environment and other co-occurring species. Studying ecosystems with an eco-evo approach, i.e., by explicitly considering species evolution and interactions, is thus an essential step to envisioning their adaptation to environmental changes. Such approach is particularly suitable for studying plankton, a community of both rapidly evolving and strongly interconnected species. In this context, Long Term Ecological Research studies (LTER) represent a promising approach to explore nature at different levels of complexity, from species to ecosystems. Herein, I examine the most recent results coming from the three-decades plankton LTER ‘MareChiara’ (LTER-MC) in the Gulf of Naples (Mediterranean Sea, Italy) and discuss their suitability in deepening knowledge on: i) evolutionary bases to plankton biodiversity (i.e., the founding property of both species and community adaptive potential); ii) ecological and evolutionary determinants of population and community dynamics; and iii) biological mechanisms behind plankton system functioning.