The microalgae polar lipids are of great interest due to their application as novel natural ingredients for the cosmetic, nutritional, and pharmaceutical industry. For this reason, the present work sought to determine the effect of the main factors in the extraction and identification of polar lipids from the microalgae Nannochloropsis oceanica and Desmodesmus asymmetricus, using Box-Behnken response surface methodology design and full factorial design, respectively. These strains from the Germplasm Bank of Aquatic Organisms (BGOA – IMARPE) were grown in a greenhouse, in 30 L bioreactors, centrifuged and lyophilized. The lipids were extracted with chloroform-methanol, fractionated and analyzed with the Waters Xevo G2-XS QTOF mass spectrometer. The maximization of total lipid extraction determined an optimal value of the mass-solvent ratio of 25 mg / 3 mL, an approximate ratio of chloroform-methanol 1:1 and an ultrasound bath time between 10 and 30 min. The main polar lipids identified for the N. oceanica microalgae were lysophophatidylcholine (LPC), diacylglyceryl-N,N,N-trimethylhomoserine (DGTS), digalactosyldiacylglycerol (DGDG), and monogalactosyldiacylglycerol (MGDG) and for D. asymmetricus were sulfoquinovosyl diacylglycerol (SQDG), LDGTS, DGTS, DGDG, and MGDG.