Algal lipids have shown promising feedstock to produce biodiesel due to higher energy content, higher cetane number and renewable nature. However, at present the lipid productivity is too low to meet the commercial needs. Various approaches can be employed to enhance the lipid content and lipid productivity in microalgae. Stress manipulation is an attractive option to modify the algal lipid content, but it faces the drawback of time-consuming production-processing and lack of information about molecular mechanisms related to triacylglycerides production in response to stress. Developing the robust hyper lipid accumulating algal strains has gained momentum due to advances in metabolic engineering and synthetic biology tools. Understanding the molecular basis of lipid biosynthesis followed by reorienting the related pathways through genomic modification is an alluring strategy which is believed to achieve the industrial and economic robustness. This review portrays the use of integrated OMIC approaches to elucidate the molecular mechanisms of strain adaptability in response to stress conditions, and identification of molecular pathways which should become novel targets to develop novel algal strains. Moreover, an update on the metabolic engineering approaches to improve the lipid production in microalgae is also provided. Microalgae are the promising photoautotrophic cell factories They can hyper-accumulate lipids but too-slow growth is a challenge The OMICs approach can be employed to elucidate lipid biosynthesis The lipid biosynthesis metabolism can be engineered in fast-growing strains Bio-preservative engineered strains can be employed in algal biorefineries This article is protected by copyright. All rights reserved.