The aim of this work was to study the properties of vertical fluorescence intensity (FI) profiles of phytoplankton pigments (chlorophyll-a, phycocyanin, phycoerythrin, and beta-carotene) using data on the phytoplankton species composition obtained during the cruise 114 of the R/V ‘Professor Vodyanitsky’. The analysis of covariance matrices of phytoplankton pigment FI profiles in the upper 50-meter layer of the Black Sea indicates that the pigment composition of phytoplankton changes with depth, which may be associated with changes in its species composition. At the same time, 80 % variability of phytoplankton pigment FI profiles in the upper 20-meter layer is described by the first eigenvector. It agrees well with direct observations of the phytoplankton species composition, indicating the dominance of one phytoplankton division in the 20-meter layer. In addition, there are regional peculiarities: for example, the average FI values of the phytoplankton pigments in the Sea of Azov are significantly higher than those in the Black Sea, which is associated with a higher concentration of phytoplankton in the Sea of Azov.