Twenty-five thraustochytrids that belong to the genus Aurantiochytrium were isolated from subtropical mangroves in Hong Kong. Although they have similar morphological and physiological characteristics, they have different colors on a yeast extract-glucose agar plate, which were largely ignored before. On the basis of the differences in their colony color, 25 Aurantiochytrium strains were further classified into pigmented and nonpigmented subgroups and their fatty acid profiles were analyzed and compared. In general, nonpigmented Aurantiochytrium strains were found to contain biomass concentrations and growth yield coefficients statistically higher than pigmented Aurantiochytrium strains (p < 0.01). Among all isolates, a significantly higher content of polyunsaturated fatty acid (PUFA, 123.41-179.64 mg/g) was found in the nonpigmented Aurantiochytrium (p < 0.01), whereas the pigmented strains contained a higher amount of saturated fatty acids. Docosahexaenoic acid (DHA) was identified as the most abundant PUFA in both nonpigmented and pigmented Aurantiochytrium. According to the result of principal component analysis, the contents and composition of saturated fatty acids and PUFAs are the major varieties to distinguish these two Aurantiochytrium groups, especially the contents of C15:0, C13:0, C16:0, C17:0, and DHA. With a rapid growth rate and high DHA yield, the strain from the nonpigmented Aurantiochytrium group was regarded as the ideal candidate for PUFA production.