Single cell oils produced by oleaginous microorganisms have attracted increasing interests as a petroleum alternative energy. Marine eukaryotes, thraustochytrids were heterotrophic, and can grow rapidly and accumulate large amount of lipids containing functional fatty acids, such as docosahexaenoic acid (DHA) in their cells body. In this investigation, thraustochytrids isolated from marine environment were cultured in the medium containing an industrial waste and an unused resource, distillery lees (Shochu kasu) to produce biofuel or functional fatty acids by microorganisms. Sixty-nine thraustochytrids and Schizochytrium aggregatum ATCC 28209 were screened for cellulase production, and the activities were detected using sodium carboxymethyl cellulose (CMC) as a substrate. Based on the screening test, strain TM02Bc identified to Schizochytrium sp. was selected for the Shochu kasu degradation test and compared with S. aggregatum ATCC 28209 previously known as a cellulase-producing thraustochytrid. Strains TM02Bc and ATCC 28209 were cultured in artificial seawater containing Shochu kasu for 15 days. The two strains could degrade Schochu kasu, especially that from sweet potato Shochu (Imo Shochu). Cellulase (CMCase) and protease activities were detected in culture supernatant of both strains, and the ratio of polyunsaturated fatty acids (PUFAs) significantly increased as a result of incubation of Shochu kasu with two strains. This preliminary study indicated that strain TM02Bc was a potent candidate for Shochu kasu treatment and fatty acid production.