The accumulation of fuel precursor-containing lipid droplets in microalgae provides a sustainable alternative to conventional fossil fuels. As large-scale development is pursued, strains that efficiently accumulate triacylglycerol (TAG) without compromised growth rates are of significant interest. We pursued increasing neutral lipid droplet yields in microalgae by inhibiting lipase activity in the diatom Thalassiosira pseudonana. Transcriptomics data identified enzymes likely involved in lipid catabolism, Thaps3_264297 (CGI-58 Tp1) and Thaps3_269487 (CGI-58 Tp2), which were downregulated during lipid accumulation. Lipase, phospholipase and acyltransferase activity were detected in CGI-58 Tp1, a homolog of Cgi-58, while this study found lipase activity in CGI-58 Tp1. To inhibit the activity of this specific lipase in T. pseudonana, antisense transgenic lines for single knock-downs of CGI-58 Tp1, and double knock-downs of CGI-58 Tp2 and CGI-58 Tp1 were generated. Both single and double knock-down transformants showed comparable growth rates in replete media and two single knock-down transformants showed twice the BODIPY fluorescence of wild -type, indicating higher lipid accumulation in stationary phase. The results indicate that downregulation of lipase activity can result in increased lipid content without affecting growth, suggesting that strains expressing the knock-down could be useful for improved biofuel production