This study focused on the evaluation of mixotrophic and heterotrophic production of phycocyanin by A. microscopica, analysis of kinetic parameters, the effect of freezing and thawing on phycocyanin yield, and nutrient removal during heterotrophic growth. During mixotrophic growth, maximum phycocyanin yield (1.50mg(phycocyanin)g(biomass)(-1)) was obtained after 12h, while the heterotrophic cultivation yielded 1.39mg(phycocyanin)g(biomass)(-1). The mixotrophic cultivation of A. microscopica showed maximum specific growth rate of 0.025h(-1), against 0.010h(-1) for the photoautotrophic cultivation, and 0.08h(-1) in heterotrophic conditions. The mixotrophic cultivation had a specific rate of phycocyanin production of 9.86mg(phycocyanin)mg(biomass)(-1)h(-1), while the photoautotrophic had 2.81mg(phycocyanin)mg(biomass)(-1)h(-1), and the heterotrophic, 49.18mg(phycocyanin)mg(biomass)(-1)h(-1). Carbon and nitrogen contents present in sugarcane vinasse were decreased in 16.69 and 15.97%, respectively, after 6h of heterotrophic growth. Thus, it was shown that the mixotrophic production of phycocyanin by Aphanothece microscopica Nageli in BG11 medium supplemented with vinasse is feasible.