The effect of mineral nutrition on growth-related metabolites and pigmentation of the filamentous Anabaena flos-aquae and Calothrix sp.PCC7601 was investigated.  Key nutrients (iron, phosphorus and nitrogen) were supplied at different concentrations compared to original BG-11 growth medium. The results showed general increase of peptide nitrogen and total sugars, chlorophyll a content and phycobiliprotein pigments content with the use of double concentration of different key nutrients. The opposite was observed for most of these parameters under half and quarter the concentration of nutrients tested in both isolates. Meanwhile, carotenoids increased under half the concentration of iron and phosphorus compared to the original concentrations of BG-11 medium but decreased at quarter concentrations of the original BG-11 medium. The effect of nitrogen limitation on growth and pigments content on A. flos-aquae was overly less severe due to the ability of A. flos-aquae to compensate for limited supply of available nitrogen through nitrogen fixation. At all reduced concentrations of key nutrients, phycoerythrin pigment predominated other phycobiliprotein pigments under white light in Calothrix sp. To further investigate the effect of mineral nutrition and light quality on phycobiliprotein pigment composition, both isolates were grown under green and red monochromatic light.  The highest content of phycroerythrin pigment was recorded under green light in both isolatesunder different nutrients treatments. Phycocyanin, on the other hand, pre-dominated other phycobiliprotein pigments in most of nutrients treatments placed under red light in Calothrix sp. This strain was more responsive in terms of alternating its phycobiliprotein composition than A. flos aquae in response to different nutrients concentration and change in light quality. Thus, this isolate seems to be a promising source for those pigments production. The study shows that growth manipulation using different nutrients concentrations and light qualities can result in differential expression of the phycobiliprotein pigments in some cyanobacterial strains. This can be used for mass production of these valuable pigments for biotechnological applications.