In order to develop microalgae as a biofuel feedstock, broadly applicable methods are needed for lipid staining and phenotypic screening of industrially relevant microalgae species. We report that treatment with ethylenediaminetetraacetic acid (EDTA) significantly enhances the fluorescence intensity for phenotypic screening of intracellular lipids in Tetraselmis suecica using Nile red (NR), a common lipophilic dye. EDTA treatment was evaluated in six different microalgae strains and was particularly effective for enhancing fluorescence intensity in T. suecica, with significant increases in fluorescence intensity compared to treatment using DMSO or glycerol. The optimal staining procedure for measuring intracellular lipids in T. suecica utilizes a 3.75mg/mL EDTA (solution in water) stained with 1.3μg/mL NR (solution in acetone) at 35°C for 5min. The ability of EDTA to improve NR staining in microalgae is attributed to the capability of EDTA to increase porosity of the cell wall. Conditions for NR lipid analysis have been optimized for six different strains of oleaginous microalgae in microplates with application for use in phenotypic screening.