<p>A set of indicators for assessing the physiological state of phycoerythrin-containing cyanobacteria of the genus <i>Synechococcus</i> is proposed. These indicators are based on the application of flow cytometry, variable fluorescence and spectral analysis methods. Quantum efficiency of photosynthesis F_V/F_m and relative electron transport rate rETR served as highly efficient metrics for assessment of the functional state of the photosynthetic apparatus of cyanobacteria. <i>Synechococcus</i> sp. BS 9001 has F_V/F_m and rETR values in the range of 0.36–0.43 and 0.3–0.35, respectively, under optimal growth conditions. F_V/F_m values of 0.25–0.35 and rETR values of 0.12–0.25 correspond to suboptimal culture growth conditions. While F_V/F_m and rETR values below 0.25 and 0.1 indicate cell death. Linear correlations between the intracellular phycoerythrin and chlorophyll concentrations in <i>Synechococcus</i> sp. and cell autofluorescence according to flow cytometry, as well as between the concentration of pigments and the optical density of the suspension were established. It was shown that under optimal growth conditions the ratios of phycoerythrobilin to chlorophyll and phycourobilin to phycoerythrobilin in the studied species <i>Synechococcus</i> sp. are 2.2–2.4 and 0.6–0.7, respectively. Under stress conditions, the values of these ratios change, reflecting the adaptation potential of the algal pigment apparatus. Modified protocols for assessing cell viability and oxidative stress level of cyanobacteria using flow cytometry in combination with vital dyes are proposed. The modified set of indicators expands the tools for assessing the viability of phycoerythrin-containing cyanobacteria both in laboratory experiments and in situ in the natural environment.</p>