The study aims on studying the microbial part of pelagic communities, giving insight on the structure of planktonic food web, and, in combination with other essential parameters of the pelagic system, leading to a further and deeper understanding of marine ecosystem of Eastern Mediterranean. The planktonic eukaryotic communities and their prokaryotic counterpart were investigated targeting at an integrated understanding of the plankton communities of the Levantine basin. This basin (eastern Mediterranean Sea) is quite intriguing due to many of its characteristics: the ultra-oligotrophic character, the noteworthy hydrographic features such the different circulation structures, and the minimum scientific attention payed in the recent years. Our main questions have been focused in investigating the composition, structure and interactions of marine planktonic communities in connections to the current circulation of the basin at the euphotic zone and the deep sea. This study combined classic marine ecology approaches such as microscopy and flow cytometry to account for absolute biomass together with NGS methods to approach biodiversity. We retained the classic planktonic ecology size-separation of the communities that will help us disentangle grazing/predation relationships between different communities' components. The further application of powerful multivariate statistical analysis is going to strengthen our results and finally lead to meaningful conclusions