The new features of the vertical phytoplankton distribution in the central and southern deep-water parts of the Caspian Sea are identified on the basis of long-term observations (2004–2012, 419 samples). Systematic study of phytoplankton in the Middle Caspian for nine years has shown that the interannual variability in the dominant summer phytoplankton complex is due to traditional species of diatoms and dinoflagellates and also coccolithophores, a new systematic group for the Caspian Sea (June 2010). It was first determined that summer phytoplankton of the deep-water parts in the Middle and Southern Caspian is similar in species, quantitative, and spatial (vertical) structure. A zone of higher phytoplankton productivity was first found in the area of the Absheron Sill. Two types of communities and their boundary were first distinguished in the vertical structure of summer phytoplankton of the deep-sea parts: warm-water and cold-water (below the thermocline). The boundary between them corresponds to the lower boundary of the seasonal thermocline (maximum depths up to 50–60 m) with the highest wet total phytoplankton biomass and chlorophyll a concentrations. The intensity of stratification of the water column by temperature mainly causes the vertical phytoplankton structure. The anomalously large deep-sea accumulations of diatoms cells containing chlorophyll (remains of winter-spring blooms) were first found in the near-bottom layers of the northern slope of the Derbent Depression. Their presence at the depths of 300–400 m is probably caused by the slope cascading. The lower boundary (500 m) of phytoplankton abundance in the Caspian Sea with chlorophyll-containing cells of fresh water green algae were registered by the authors for the first time in the central areas of the Derbent and South Caspian depressions. This phenomenon was caused by the contribution of cold Caucasus rivers through a system of submarine canyons from the shelf to the deep sea areas.
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