This work is part of a megaproject that seeks to isolate microalgae of the Chlorophyta division native to Norte de Santander and identify their potential applications such as lipid production to be used as biofuel. Here we present the isolation of 11 microalgae strains from the Chlorophyta division found in two different wastewater environments. The collected strains were cultivated in selective media and purified through serial dilutions, depletion culture, and application of penicillin and gentamicin. Biomass production was evaluated and two strains were selected: CHL1 (Chlorella sp.) and DES1 (Desmodesmus sp.). The strains were cultivated on wastewater and PCG media (control), and their biomass concentration and lipid content were measured. Both strains reached similar biomass concentrations compared to their respective controls (CHL1 PCG 1.5 mg/L ± 0.035 mg/L, CHL1 AR 1.68 mg/L ± 0.036, DES1 PCG 1.66 mg/L ± 0.007, DES1 AR 2 mg/L ± 0.03) and their lipid content was slightly higher compared to their controls. The results show that the isolated and evaluated strains may have potential to be lipid producers, since their environmental and nutritional conditions have not been modified yet and adaptation may improve the production yield of lipids.