Microalgal biofuels are desirable alternatives for traditional liquid fuels, but further improvements of productivity are necessary for microalgal biofuels to be economically feasible. As strategies for improving lipid productivity, repression of lipid degradation has a great potential because the lipid accumulation level is determined by a balance between lipid synthesis and degradation. However, studies of lipid degradation and its primary functioning enzyme triacylglycerol (TAG) lipases in microalgae are currently limited. In this study, we report the comprehensive analysis of TAG lipases in the oleaginous diatom Fistulifera solaris JPCC DA0580. First, we confirmed that TAGs in the lipid accumulation organelles, oil bodies, were degraded when the cells were transferred from the nutrient depleted conditions to nutrient replete condition. Further analysis revealed that, after eicosapentaenoic acid (C20:5n-3)-containing TAGs are were degraded, its molecular skeletons were likely to be recycled to produce glycolipids and phospholipids for chloroplast regeneration and cell growth, respectively. Next, we searched putative TAG lipase genes from the draft genome sequence of F. solaris, and discovered 42 candidates based on the amino acid sequence homology analysis. Subsequent transcriptome analysis revealed that 16 of the 42 lipase genes were up-regulated during lipid degradation. Among the up-regulated lipases, a number of enzymes were predicted to localize in endoplasmic reticulum which is closely associated to the lipid accumulation organelles, oil bodies. Our study provided new insights of lipid degradation in oleaginous microalgae, and putative TAG lipases which could be candidates for metabolic engineering in future study to improve microalgal lipid productivity.