Microalgae were originally considered as sources of long-chain polyunsaturated fatty acids (PUFAs), mainly for aquaculture purposes. However, based on the fact that their fatty acids (FA), stored as triacylglycerides (TAG), can be converted into biodiesel via a transesterification reaction, several microalgal species have emerged over the last decade as promising feedstocks for biofuel production. Elucidation of microalgae FA and TAG metabolic pathways is therefore becoming a cutting-edge field for developing transgenic algal strains with improved lipid accumulation ability. Furthermore, many of the biomolecules produced by microalgae can also be exploited. In this chapter, we describe recent advances in the field of FA and TAG pathways in microalgae, focusing in particular on the enzymes involved in FA and TAG synthesis, their accumulation in lipid droplets, and their degradation. Mention is made of potentially high-value products that can be obtained from microalgae, and possible molecular targets for enhancing FA and TAG production are outlined. A summary is provided of transcriptomics, proteomics, and metabolomics of the above-mentioned pathways in microalgae. Understanding the relation between anabolic and catabolic lipid enzyme pathways will provide new insights into biodiesel production and other valuable biomolecules obtained from microalgae.