Objective To study the severe acute respiratory syndrome (SARS)-associated coronavirus genotype and its characteristics. Methods A SARS-associated coronavirus isolate named Z J0. was obtained from throat swab samples taken from a patient in Hangzhou, Zhejing province. The complete genome sequence of Z J0. consisted of 29 715 bp (GenBank accession: AY297028, version: gi: 30910859). Seventeen SARS-associated coronavirus genome sequences in GenBank were compared to analyze the common sequence variations and the probability of co-occurrence of multiple polymorphisms or mutations. Phylogenetic analysis of those sequences was done. Results By bioinformatics processing and analysis, the 5 loci nucleotides at Z J0. genome were found being T, T, G, T and T, respectively. Compared with other SARS-associated coronavirus genomes in the GenBank database, an A/G mutation was detected besides the other 4 mutation loci (C: G: C: C/T: T: T: T) involved in this genetic signature. Therefore a new definition was put forward according to the 5 mutation loci. SARS-associated coronavirus strains would be grouped into two genotypes (C: G: A: C: C/T: T: G: T: T), and abbreviated as SARS coronavirus C genotype and T genotype. On the basis of this new definition, the Z J0. isolate belongs to SARS-associated coronavirus T genotype, first discovered and reported in mainland China. Phylogenetic analysis of the spike protein aene fraaments of these SARS-associated coronavirus strains showed that the GZ0. isolate was phylogenetically distinct from other isolates, and compared with groups F1 and F2 of the T genotype, the isolates of B J01 and CUHK-Wl were more closely related to the GZ0. isolate. It was interesting to find that two (A/G and C/T) of the five mutation loci occurred in the spike protein gene, which caused changes of Asp to Gly and Thr to lie in the protein, respectively. Conclusion Attention should be paid to whether these genotype and mutation patterns are related to the virus's biological activities, epidemic characteristics and host clinical symptoms.