Chlamydia felis is a causative agent of acute and chronic conjunctivitis and pneumonia in cats (feline chlamydiosis). The polymorphic membrane proteins (pmp) are a group of genes thought to encode members of the unique chlamydial pmp family. This study is aimed at determining the occurrence of C. felis and pmp by PCR in eye conjunctiva and oral swabs in 156 cats from 2 shelters from Brazil. The cats are of unknown origin and were collected via public. The observed occurrence of C. felis was 7.41% in the first cattery, 46.15% in the second. Four samples, 2 from each cattery, were amplified for 12 pmp genes. PCR products ranging from 525 to 698 base pairs of pmp genes 7, 9–11, 13–20 were sequenced. The partial sequences were compared to each other and between samples collected in GenBank. The identities of sequences analyzed were 100%, with exception of pmp 9, which showed 99% identity with Cello strain from the USA (access DQ652569). We conclude, therefore, no regional differentiation when compared to strains from other countries (UK, USA and Japan) and neither with the strains between the two catteries sampled.