The harvest of oil from large-scale algal cultivation has become an attractive source of alternative and sustainable biofuel to replace traditional fossil fuels. Understanding how algae store and breakdown their synthesized oils sequestered within specialized organelles known as lipid bodies is key to improving algae oil production. My study is to: a) propose a model alga, b) cytologically probe lipid body architecture, c) and document lipase activity gaining access to oils within lipid bodies. To select a model alga for my studies, I conducted a survey of my laboratory’s algae culture collection looking at organisms across a variety of taxa, lipid body morphology, spatial arrangement, and total number of lipid bodies. BODIPY 505/515, a lipophilic dye, was used to integrate the lipid bodies of these organisms. Chrysochromulina sp. was identified as the best model organism for its simple compliment of two large lipid bodies. Counterstained lipid bodies indicate a strong co-localization of an endoplasmic reticulum membrane with lipid bodies. Fluorescein diacetate was used as a fluorescent indicator for lipase activity. Over a 24-hr time course study, flow cytometric data showed fluorescein diacetate fluorescence increasing as BODIPY 505/515 fluorescence decreased. Cytological studies also show fluorescein diacetate localizing to lipid bodies during its peak fluorescence. These results indicate an endoplasmic reticulum membrane surrounds Chrysochromulina sp.’s lipid bodies and lipases are involved in gaining access to fatty acids through the endoplasmic reticulum membrane. In determining effective algal lipid harvesting protocols it is paramount to first understand cellular lipid usage. Developing the most efficient methods of converting algal lipid bodies to biofuels will accelerate the viability of the global transition to alternative fuel sources.