Calanoid copepods and pelagic tunicates are the two most abundant groups of mesozooplankton with highest impact on pelagic ecosystems. They are main grazers of phytoplankton important for their ability to modulate phytoplankton blooms. They are also major secondary producers and important source of food for higher trophic levels. Genetic diversity of these groups was not investigated in the South Adriatic and for pelagic tunicates there is very few data in general. In order to investigate large scale genetic diversity of these groups in the Adriatic we plan to use metabarcoding approach. Metabarcoding is revolutionary method for assessing biodiversity and determining community composition by sequencing orthologous DNA regions of virtually all species within the sample using massive parallel high-throughput sequencing techniques (HTS). For this purpose we will create a database of main barcoding genes such as COI, 18S as well as ITS region for calanoid copepods and pelagic tunicates to serve as a reference for metabarcoding studies. The aim of our project is to use HTS for genetic characterization of Adriatic mesozooplankton populations, to determine differences in their genetic composition between different parts of the Adriatic which differ in their depth, magnitude of seasonal variation in salinity and temperature (such as North and South Adriatic) and distance from the shore and. Special attention will be paid to genetic characterization of deep sea populations and populations in enclosed coastal environments which are known to harbour distinct zooplankton, such as Mljet lakes. The project will gather comprehensive data on the state and interactions of Adriatic zooplankton communities which would serve as a basis for better environmental management. Furthermore, we will assess the potential of HTS as a monitoring technique for non-indigenous species, their dispersal and impact on zooplankton community.