Microalgae are promising alternative feedstocks that can be used to produce biofuels and replace conventional fossil fuels. In order to increase the lipid production of microalgae, strain development via genetic engineering is required. To date, metabolic engineering studies have mainly focused on lipid synthesis pathways. However, the complicated metabolic pathways that exist in many organelles along with limitations of genetic engineering tools have made it difficult to obtain desirable microalgal strains. As an alternative strategy, we tried to increase carbon flux into fatty acid synthesis by overexpressing the NADP-dependent malic enzyme, NsME1, in Nanno-chloropsis salina. We found that the biomass and fatty acid methyl ester (FAME) contents were increased in NsME1 overexpressing transformants, such that the FAME yield of the top-producing NsME1 transformant was 53% higher than the wild type. To understand the effects of NsME1 on lipid production, we analyzed the total carbon concentration and NADPH/NADP ratio, which were found to be enhanced in the transformants. We also investigated mRNA expression levels of genes involved in C4-like carbon concentrating mechanism and fatty acid synthesis by quantitative real-time PCR, and confirmed their positive contribution to fatty acid production. Taken together, our results demonstrate that overexpression of NsME1 could simultaneously improve the carbon concentration and reducing power in cells, thereby increasing the lipid and FAME yields of Nannochloropsis salina. We suggest that NsME1 can serve as a promising genetic target for enhancing lipid-based bio-products in Nannochloropsis and potentially other industrial microalgae.