is an excellent unicellular bait for the larvae of many aquaculture animals. Thus, screening for strains with rapid growth rate and high content of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) is very important for the breeding of aquaculture animals. However, most of the strains in China have been derived from a common ancestor called have been developed after a long duration of geographical isolation. Whether the traits of these strains have changed or not remains unknown. In order to evaluate the status of the phenotypic traits of different geographic isolates for future selective breeding, comparative analysis of five strains of (FACHB-861, OA3011-QD, OA3011-LK, OA3011-AY, and OA3011-LZ) with regard to their taxonomy, growth, and fatty acid composition was conducted. Different strains were cultured under identical conditions for six days until they reached a stationary phase. Genomic DNA was extracted for polymerase chain reaction sequencing of the 18S rDNA gene. The OD₆₆₀ was recorded daily for plotting a growth curve. When the cultures reached stationary phase, they were harvested by high-speed centrifugation for biomass determination and fatty acid analysis by using gas chromatography. Phylogenetic analysis of the 18S rDNA gene suggested that FACHB-861 was distantly related with the OA-3011 strains. OA3011-LK, OA3011-AY, and OA3011-LZ had identical 18S rDNA sequences, but the 18S rDNA sequence of OA3011-QD differed from that of the other OA-3011 strains at one position, resulting in a single base substitution. The growth curve showed that the five strains reached stationary phase at different times. FACHB-861 showed a distinct pattern of growth, unlike the other four OA-3011 strains. The final biomass concentrations were significantly different between FACHB-861 and OA-3011 strains as well as among OA3011-LK, OA3011-AY, and OA3011-LZ (<0.05), whereas the growth rates were not significantly different among the strains (>0.05). The total fatty acid content of FACHB-861 and OA3011-LZ were significantly lower than that of OA3011-LK, OA3011-QD, and OA3011-AY (<0.05). The fatty acid profile of FACHB-861 was remarkably different from that of the OA-3011 strains. However, a conspicuous variation in fatty acid compositions was also observed among OA-3011 strains, indicating a wide and frequent quantitative phenotypic variation among the strains of . These variations resulting from geographic isolation might provide a feasible method for the selective breeding of strains. According to the screening criteria such as growth rate or DHA, EPA, and polyunsaturated fatty acid content, our preliminary analysis showed that OA3011-LK, which has the highest growth rate, and OA3011-QD, which contains the highest amount of DHA, are promising candidates for further screening.