The lipid composition in terms of the amount of neutral lipids, free fatty acids and polar lipid content is of great importance to make full use possible of this fraction and to define the suitability of its application, either as a raw material for fuel production, nutraceutical purposes or feed. In addition to the fatty components present in the lipid extract, other components may be included, such as: carotenoids, pigments and sterols. The microalgae studied in this work, Scenedesmus sp. and Desmodesmus sp., were subjected to the same growth conditions and evaluated for lipid content, quantification and diversity of lipid components as well as its fatty acid profile. For lipid determination two extraction methods were compared: the J: Schmid-Bondzynski-Ratzlaff and Bligh & Dyer method. For Desmodesmus sp. 5.43% ± 0.41% and 9.18% ± 0.33% of lipids were obtained on an ash-free dry weight basis and for Scenedesmus sp. 12.46% ± 0.38% and 8.16% ± 0.42% of lipids were obtained on an ash-free dry weight basis using for both methods J: Schmid-Bondzynski-Ratzlaff and Bligh & Dyer, respectively. For the identification of the main lipid components present in the extracts, the Thin layer chromatography (TLC) technique was used. This made it possible, using a simple and inexpensive method, to identify the compounds extracted by different extraction methods, that is, it was possible to verify the selectivity of the different extraction methods. In addition, it has been shown that using these methods, widely described in the literature as methods of extracting lipids in practice, extracts a wide diversity of compounds. The major lipid class for both microalgae was fatty acids with amounts between 23.62% - 38.02%. The triglycerides percentage in biomasses without chemical treatment did not exceed 18.26%. In the lipid extract obtained with Bligh & Dyer, the microalgae Desmodesmus sp. presented 55.26% of unsaponifiable material, higher than the amount present using the same extraction method for Scenedesmus sp. 49.06%. Among the main unsaponifiables identified are hydrocarbons (carotenes) and sterols esters. The acid treatment of biomass, method J: Schmid-Bondzynski-Ratzlaff, showed selectivity of 72.84% and 76.66% for obtaining fatty material from the microalgae Desmodesmus sp. and Scenedesmus sp., respectively. The results showed that depending on the method used for extraction, the lipid fraction will be different in relation to the percentage of fatty components.