Glucose is the substrate most widely used as exogenous carbon source for heterotrophic cultivation of cyanobacteria. Due to limited information about the use of different carbohydrates as carbon sources to support cyanobacterial heterotrophic metabolism, the objective of this work was to evaluate different monosaccharides (arabinose, fructose, galactose, glucose, mannose and xylose), disaccharides (lactose, maltose, sucrose and trehalose) and polysaccharides (carboxymethylcellulose, cassava starch, Hi-maize(®), maltodextrin Corn Globe 1805(®) and xylan) as exogenous carbon source for heterotrophic culture of cyanobacterium Phormidium sp. The batch cultivation using fructose as organic carbon source resulted in the highest (p < 0.05) cell biomass (5,540 mg/L) in parallel with the highest (p < 0.05) substrate yield coefficient (0.67 mg(biomass)/mg(fructose)). Mannose was the carbon source with the highest (p < 0.05) substrate consumption rate (3,185.7 mg/L/day) and maltodextrin was the carbohydrate with major potential to produce biomass (1,072.8 mg(biomass)/L/day) and lipids (160.8 mg(lipids)/L/day). Qualitatively, the fatty acid profiles of the lipid extract from Phormidium sp. showed predominance of saturated chains for the cultures grown with most of the carbon sources, with the exception of the ones grown with xylose and maltodextrin.