Abstract Some cyanobacteria species have a high capacity for accumulating phycobiliprotein contents in their cells. However, there is a lack of information on the screening of tropical freshwater cyanobacteria, particularly phycobiliproteins. In addition, it is unclear which cellular factor of cyanobacteria (morphological and/or growth) could affect phycobiliproteins production. Hence, the objectives of this study were to isolate and screen the Malaysian indigenous cyanobacteria for the desired growth, biomass and pigment contents of the isolated cyanobacteria and determine the main internal factor that contributed to the variation of phycobiliproteins. The surface/volume (S/V) ratio, specific growth rate, biomass productivity and pigment contents were analysed. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) were applied to distinguish the factor responsible for phycobiliprotein variations in cyanobacteria. Synechocystis sp. demonstrated significantly higher (P < 0.05) specific growth rates and biomass productivity than the other cyanobacteria. For the phycobiliprotein contents, Arthrospira sp., Pseudanabaena sp., and Synechococcus elongatus showed significantly higher (P < 0.05) amounts of phycocyanin (PC), phycoerythrin (PE) and allophycocyanin (APC), respectively, than the other cyanobacteria. The present study suggested that Arthrospira sp., Pseudanabaena sp. and Synechococcus elongatus are suitable candidates for commercial production of PC, PE and APC sources, respectively. Moreover, the current findings showed that the phycobiliprotein contents of cyanobacteria were strain-dependent. Further analyses are required to examine the toxicity of these cyanobacteria to ensure these pigments are safe to be consumed or utilised.