Investigators from various fields of study have derived from searching for an alternative biofuel in crops such as soybeans and corn that could replace the current use of fossil fuels, because of their slow production rate. Instead, a new wave of scientists has identified the potential and benefits that microalgae have over crops. Although, the cultivation of microalgae also has its own complications that need to be managed before mass production. When searching for promising species, one of the difficulties encountered is the lack of a rapid tactic to determine the neutral lipid content in microalgae. Traditionally, lipid content assessment has been examined by the gravimetric method, which is cost and labor intensive and time consuming. Nile red staining have proved to help in the quantification of intracellular lipid bodies in microalgae and several protocols have been developed. However, most of these protocols work with a limited number of species and a suitable staining methodology has been difficult to develop with thick cell wall species. We aimed to developed a protocol for staining lipids in Botryococcus sudeticus, a thick cell wall microalgae, involving Nile Red addition coupled with cell wall break. Three different procedures were examined and compared with the traditional Nile Red staining method, as described previously. Future experiments will evaluate these procedures with nitrogen starved cells, condition that promotes lipid accumulation.