Aurantiochytrium are protists found in marine and estuarine environments, known for producing high quantities of omega-3 fatty acids, particularly docosahexaenoic acid (DHA). The commercial viability of this species is currently hindered by the lack of reliable screening methods for the rapid identification of strains with high DHA content. This study developed a high-throughput screening platform based on the sulfo-phospho-vanillin (SPV) reaction, which produces a pink chromophore upon reacting with C-C double bonds in lipids. Analysis of 200 strains derived through the UV mutagenesis of the Aurantiochytrium limacinum strain BL10 revealed 7 strains that exhibited significantly elevated SPV reactivity, compared to the naïve strain (P <
0.01). Gas chromatography-mass spectrometry analysis revealed that in 4 of the 7 strains, DHA levels were significantly higher than those of the naïve strain. Among those 4 strains, the SPV reactivity values of two strains were precisely correlated with their DHA/DPA content. The SPV reaction protocol proposed in this paper has considerable potential for the high-throughput screening of Aurantiochytrium strains particularly those derived through UV mutagenesis.