In order to understand the molecular characteristics of a feline infectious peritonitis virus (FIPV) isolated in Shanghai, genes encoding three non-structural proteins ORF3 (3a, 3b and 3c), ORF7 (7a and 7b) and S2 of three FIPV strains were amplified by RT-PCR, sequenced and analyzed. On ORF3a, ORF3b and ORF3c substitutional mutations leading to amino acid changes were identified. On ORF7a gene, mutations were found at the 47th amino acid. A 3 nt deletion in ORF7b gene was identified in one strain. At the S1/S2 cleavage site of the S gene, there were continuous R-R-S/A-R-R-S sequence modules, which were consistent with the protein sequence characteristics of the FIPV cleavage site. The methionine was replaced by leucine at 1 045th amino acid in all samples. The phylogenetic tree showed that the sequences of FIPV ORF3c, ORF7b and S2 genes were closely related to serotype Ⅰ strains, indicating that the three strains belonged to serotype Ⅰ. The mutations in S genes may be involved in the change of tissue tropism in FCoV.