Microalgae have an excellent potential for producing valuable natural products, including biofuels. Therefore, it is imperative to explore and document the existing microalgal flora and utilize their potentials to cope the increasing human needs. The present work aims at exploring and characterizing newly isolated microalgae from desert Cholistan, a habitat with myriad algal diversity. Light microscopy, scanning electron microscopy, and molecular phylogenetic approaches were used for specieslevel identification. Characterization and growth optimization of Scendesmus sp. were analyzed under three different growth modes to determine the most favorable conditions for increasing biomass, growth rate, and lipid content. The results revealed that mixotrophic (MT) mode significantly increases photosynthetic activity, growth rate, and lipid content with glycerol as supplement carbon source. The investigated Scenedesmus dimorphous produced a maximum dry weight of 1.73 g L −1 , improved fatty acid methyl esters profile and yield lipid up to 40% of DCW (68 g L −1 ) under MT mode, which is almost double to that of photoautotrophic cultivation. The glycerol availability in medium has been identified as the critical element for boosting growth and lipid content. Thus, it can reduce the cost of biofuel production. K E Y W O R D S biofuels, biomass, indigenous desert species, phylogeny, SEM morphology