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This study presents experimental measurements of the absorption and scattering cross sections and the spectral complex index of refraction of filamentous cyanobacteria. Filamentous heterocystous cyanobacterium Anabaena cylindrica was chosen as a model organism. Its filaments consisted of long chains of polydisperse cells. Their average mass scattering and absorption cross sections were measured from 400 to 750 nm at four different times during their batch growth in medium BG-11(-N) under 3000 lux of white fluorescent light. The effective real (or refraction index) and imaginary (or absorption index) parts of the complex index of refraction were retrieved using an inverse method based on a genetic algorithm. The microorganisms were modeled as infinitely long and randomly oriented volume-equivalent cylinders. The absorption index featured peaks corresponding to chlorophyll a (Chl a) at 436 and 676 nm and phycocyanin (PCCN) at 630 nm and a shoulder around 480 nm, corresponding to photoprotective carotenoids. The absorption peaks of Chl a and PCCN concentrations increased and the shoulder due to carotenoids decreased in response to photolimitation caused by biomass growth. Subsequent nitrogen limitation caused the PCCN absorption peak to decrease significantly due to degradation of PCCN as an endogenous source of nitrogen for nitrogenase maintenance and synthesis, as confirmed by increasing heterocyst differentiation. The results can be used for predicting and optimizing light transfer in photobioreactors for wastewater treatment and ammonia or biofuel production.