AbstractCharacterization of hydrobionts concentrations in coastal and deep‐water areas of the Black Sea during the summer was carried out to analyse features related to the vertical distribution of bioluminescence intensity in the phytoplankton community. The thermohaline structure of the water and regional characteristics of eddy formations determined from satellite measurements of sea level anomalies were taken into account. Integral intensity of bioluminescence of hydrobionts (IIBH) was used to comparatively assess total biomass variability and the numbers of hydrobionts in the considered regions. The highest IIBH, averaging 37 830 pW·cm−2·L−1, was observed at stations located on the south‐western shelf of the Crimea; high levels of bioluminescence intensity of hydrobionts in this layer were located at depths of 15–23 m. For stations located in the Kerch pre‐strait area, most of which were in the divergence zone, the average IIBH was quite high (30 530 pW·cm−2·l−1), second only to the value recorded for the shallow south‐western shelf.