Restriction fragments containing the major outer-membrane protein (MOMP) gene from two nonhuman (rodent) strains of Chlamydia trachomatis, the mouse pneumonitis (MoPn) strain and the SFPD strain isolated from hamsters with transmissible proliferative ileitis, were cloned and sequenced. The MOMP genes of both MoPn and SFPD encode an identical 22-amino acid leader peptide and mature polypeptides of 365 and 382 amino acids, respectively. Alignment of the MOMP genes of the two rodent strains revealed 91% identity. By comparison with other known chlamydial MOMP gene sequences, there was 80%-83% identity with human biovars strains of C. trachomatis, and there was 69%-70% identity with C. psittaci and C. pneumoniae strains. The main differences in these sequences were clustered into four variable domains. A minimum-length evolutionary tree was constructed on the basis of the MOMP gene variable positions by using PIMA package software. The minimum mutation distances indicated that (i) the MOMP genes of all chlamydial strains may have evolved from a common ancestor; (ii) all the strains of C. trachomatis compose one of the subtrees, and strains of C. psittaci and C. pneumoniae compose the other subtree; and (iii) in the C. trachomatis subtree, the human and the rodent strains are divided into two clusters. The branching pattern of this evolutionary tree is generally consistent with current classification based on serological, morphological, and other biological characteristics.