Complete nucleotide sequences were determined by cDNA cloning of peplomer (S), integral membrane (M) and nucleocapsid (N) genes of feline infectious peritonitis virus (FIPV) type I strain KU-2, UCD1 and Black, and feline enteric coronavirus (FECV) type II strain 79-1683. Only M and N genes were analyzed in strain KU-2 and strain 79-1683, which still had unknown nucleotide sequences. Deduced amino acid sequences of S, M and N proteins were compared in a total of 7 strains of coronaviruses, which included FIPV type II strain 79-1146, canine coronavirus (CCV) strain Insavc-1 and transmissible gastroenteritis virus of swine (TGEV) strain Purdue. Comparison of deduced amino acid sequences of M and N proteins revealed that both M and N proteins had an identity of at least 90% between FIPV type I and type II. The phylogenetic tree of the M and N protein-deduced amino acid sequences showed that FIPV type I and type II form a group with FECV type II, and that these viruses were evolutionarily distant from CCV and TGEV. On the other hand, when the S protein-deduced amino acid sequences was compared, identity of only about 45% was found between FIPV type I and type II. The phylogenetic tree of the S protein-deduced amino acid sequences indicated that three strains of FIPV type I form a group, and that it is a very long distance from the FIPV type II, FECV type II, CCV and TGEV groups.Key words: Feline infectious peritonitis virus, Feline enteric coronavirus, Amino acid sequence Feline infectious peritonitis virus (FIPV), family Coronaviridae, genus Coronavirus, causes a chronic, progressive, immunologically mediated disease in domestic and exotic cats.The family Coronaviridae is divided into 3 distinct antigenic groups on the basis of serologic tests (18). One group contains mouse hepatitis virus, neonatal calf diarrhea coronavirus, human coronavirus OC43, hemagglutinating encephalomyelitis virus of swine and rat coronavirus. The second group contains avian infectious bronchitis virus. The third group consists of human respiratory coronavirus 229E, transmissible gastroenteritis virus (TGEV) of swine, porcine respiratory coronavirus, canine coronavirus (CCV), FIPV and feline enteric coronavirus (FECV). By using monoclonal antibodies we have shown the existence of at least 2 serotypes of FIPV, and the antigenicity of type II strain of FIPV and FECV were closer to TGEV and CCV than to type I FIPV (7,8). Both types I and II FIPV cause infectious peritonitis in cats, and the pathogenicity of type II FIPV is greater than that of type I FIPV (25). However, in the field, the prevalence of FIPV type I is high, and about 70% of feline cases of FIP are due to infection with type I (9).FIPV is an enveloped RNA virus with a single-stranded positive-sense RNA genome and the virions consist of three main structural proteins, peplomer (S) glycoprotein, integral membrane (M) glycoprotein and nucleocapsid (N) protein. The virus genome is at least 20 kilobases