Aim. For the first time, flow cytometry has been used to study the structure and functional characteristics of bacterio‐, pico‐ and nano‐ phytoplankton in the Middle Caspian during the bloom period in early September 2022.Water samples were taken at different horizons (from the surface to the bottom layer) at a series of stations along the western coast of the Caspian Sea on the border between its northern and central parts to quantitatively assess heterotrophic bacterioplankton, picophyto‐ and nanophy‐ toplankton. Sampling was undertaken in early September 2022 under summer hydrological conditions with water surface temperatures ranging from 24.7°C to 26.7°C. Sample analysis was performed using flow cytometry.Extremely high concentrations of picophytoplankton (up to 1.8×105 cells/mL), probably of Synechococcus picocyanobacteria, were detected off the northwestern coast of the Middle Caspian. Very high values of nanophytoplankton abundance (up to 1.6×105 cells/mL), dominated by small flagellates, were also found. A clear spatial uncoupling of pico‐ and nanophytoplankton was revealed. Maximum levels of nanophytoplankton were confined to the area of intensive phytoplankton blooming with high concentrations of chlorophyll a, while picophytoplankton reached peak abundance further south, outside this area. The influence of the thermocline on the vertical structure of microbial communities was detected. The concentrations of picophytoplankton and the proportion of physiologically active HNA‐bacteria decreased sharply under the thermocline.The results obtained indicate the leading role of the smallest phototrophs in the Caspian pelagial and emphasise the need for further comprehensive studies of Caspian microbial communities using modern methods.