Biodiesel production from microalgae triacylglycerols is growing, because this feedstock is a more sustainable and advantageous alternative. In this study, we isolated and identified fourteen strains of native microalgae from the Peruvian Amazon. These strains showed great heterogeneity in biomass productivity, lipid productivity and lipid content, and thus, three of them (Acutodesmus obliquus, Ankistrodesmus sp. and Chlorella lewinii) were selected for further evaluation under culture of nitrogen-sufficient (+N) and nitrogen-deficient (-N) Chu medium No. 10. These microalgae species showed modifications in biomolecule content (protein, lipid and carbohydrate) with a pronounced increase of lipids and carbohydrate and a decrease of protein content under stress culture. Furthermore, the fatty acid profile was peculiar for each species, and these patterns showed evident changes, particularly in the proportion of saturated and monounsaturated fatty acids. The results of this research suggest that the isolated native microalgae, from the Peruvian Amazon, could be suitable candidates for biodiesel production.