A filamentous cyanobacterium, Trichormus sp. IMU26, capable of rapid growth and high phycobiliprotein (PBP) production under N-2-fixing conditions was isolated. The strain has been maintained in N-free BG-11 medium for more than 20 months upon isolation. Nitrogen supply resulted in higher soluble protein and saccharide content but a lower growth rate and PBP production in Trichormus sp. IMU26. Short-term N-P deprivation induced PBP production with no clear change in growth while growth and PBP content decreased in the longer incubation period. Induction of PBP production in N-P-deprived cells was characterized by FTIR analysis and change in carotenoid-pigment interactions. Rapid induction of zeaxanthin and beta-carotene production and slight reduction of echinenone and canthaxanthin levels might be associated with increased PBP levels in short-term N-P deprivation of Trichormus sp. IMU26. Overall, long-term diazotrophic growth of N-2-fixing cyanobacteria may increase the PBP yield.