To characterize the hypothetical protein CT249 using antibodies raised with CT249 fusion protein. The open reading frame (ORF) coding for CT249 in the Chlamydia trachomatis serovar L2 genome was cloned into the pGEX-6p2 vector using the restriction enzymes BamH I and Not I. The recombinant plasmid pGEX-6p2-CT249 was transformed into XL1-blue bacteria and the gene CT249 was expressed as fusion proteins with the glutathione-s-transferase (GST) tagged to the N-terminus. The GST-CT249 fusion protein was used to immunize mice and the mouse anti-fusion protein antibody was used to localize the endogenous CT249 protein in Chlamydia-infected cells using an indirect immunofluorescence assay (IFA). The CT249 gene with 351bps in length was successfully cloned and expressed as GST fusion protein with molecular weight of 38.2kDa. The anti-fusion protein antibodies produced from mice detected the hypothetical protein CT249 in the inclusion membrane of Chlamydia trachomatis-infected cells. Using antibodies raised with GST-CT249 fusion protein, the hypothetical protein CT249 have been identified as a Chlamydia trachomatis inclusion membrane protein. Given the potentially important role of inclusion membrane proteins in chlamydial interactions with host cells, this finding has provided a useful tool for further understanding the mechanisms of chlamydial intracellular parasitism.