Physiological properties of organism, such as the number of chromosomes, genome size, fatty acid profile and the activities of desaturases and elongases were investigated for four different Thraustochytrium species. The investigation revealed that Thraustochytrium aureum could synthesize a significant level of polyunsaturated fatty acids (PUFAs), particularly docosa-hexaenoic acid (DHA), when compared to the other three Thraustochytrium species tested. A higher level of saturated fatty acids was observed by T. striatum followed by Thraustochytrium sp. ATCC 26185. The PUFA accumulation rate was higher in the n-3 than in the n-6 pathway. A comparison of the activities for these desaturases and elongases of the four different species were also studied. Further, the electrophoretic karyotypes of Thraustochytrids were separated by pulsed-field gel electrophoresis (PFGE). The separation condition of PFGE was developed to obtain the different chromosomes from the various Thraustochytrium species. The number of chromosomes in T. aureum, T. striatum, Thraustochytrium sp. ATCC 20891 and Thraustochytrium sp. ATCC 26185 were 13, 17, 10, 8, and the whole genome size of those species were estimated to be 12.9, 11.7, 11.3, and 9.93 Mbp, respectively.