At present there is no consistent approach for the definition of Good Environmental Status (GES) and targets in the Mediterranean Sea, especially for Biodiversity Descriptors, according to the Article 12 of the Marine Strategy Framework Directive (MSFD). The use of plankton indicators in the Mediterranean Sea refers mostly to pelagic habitats in coastal waters and to case studies connected with environmental pressures, e.g. in the Adriatic, Aegean etc. The aim of this review is to study the existing biodiversity indicators for different plankton groups in order to compare GES definitions for the Biodiversity Descriptor and identify the relevant gaps and priority needs to improve coherence for the MSFD implementation across the Mediterranean. For these purposes, we focus on plankton indicators for phytoplankton, zooplankton and prokaryotes. Regional conventions (OSPAR, HELCOM, Barcelona and Bucharest Conventions) have long considered phytoplankton as a key element for integrated assessment systems. Phytoplankton biomass, community composition, abundance, frequency and intensity of blooms are used for such assessment purposes. Chlorophyll a still remains the most widely used indicator mostly thanks to its time saving, cost-effective and reproducible analytical methods that provide easily comparable datasets. Despite some integrated indices proposed for phytoplankton in the literature at the Mediterranean level, a number of constrains still prevent their wide use. Regarding zooplankton communities, commonly used indicators have a taxonomic base while recently size structure and biomass can provide a valuable index of zooplankton population dynamics and ecosystem production. Jellyfish blooms' occurrence and frequency are also considered important zooplankton Highlights ► Low coherence for GES definitions in Mediterranean plankton communities was found. ► Phytoplankton is a key element for assessment systems of MSFD and Regional Conventions. ► GES targets are based only on Chlorophyll a thresholds in the Mediterranean so far. ► Quantitative GES targets for zooplankton in Mediterranean exist only in Slovenia. ► Gaps mostly focus on lack of thresholds and baselines for many biodiversity indicators.