Cyanobacteria are unique prokaryotes, which are capable to perform oxygenic photosynthesis. Within these organisms, phycobilisomes (PBS) act as an antenna of the photosynthetic pigment apparatus. Phycobilisomes contain several phycobiliproteins (PBP): phycoerythrin (PE), phycocyanin (PC), allophycocyanin (APC) and phycoerythrocyanin (PEC). The application of phycobiliproteins in the biotechnology, food industry and medicine during the last years is rapidly increasing. The aim of our study was to assess the qualitative and quantitative content of phycoerythrin, phycocyanin, allophycocyanin and phycoerythrocyanin in 14 cyanobacterial strains kept in Plovdiv Algal Culture Collection (PACC) and 4 strains purchased from the Culture Collection of Autotrophic Organisms (CCALA). Our data demonstrated that three strains of Microcoleus autumnalis (PACC 5505, PACC 5522 and PACC 5527) have high potential to produce phycoerythrins (0.132, 0.201 and 0.136 mg/mL, respectively). Similarly, one Microcoleus autumnalis strain (PACC 5522) and one strain of Leptolyngbya boryana (CCALA 084) are suitable for biotechnological production of phycocyanins (0.051 and 0.264 mg/mL, respectively) as well as allophycocyanins (0.102 and 0.171 mg/mL, respectively). In addition, the data about the pigment content could be used as a biochemical marker for taxonomic purposes within the group.