The whole genome sequences of pathogenic bacteria and the host genome such as human has provided a Subtractive genomic approach, which can be used to identify potent vaccine and drug targets. In the present study subtractive genomic approach has been used to identify therapeutic target in Chlamydia trachomatis. C.trachomatis infection is now the most common sexually transmitted disease worldwide. The BlastP search against Homo sapiens revealed 551 non-homologous protein sequences out of 874 in C.trachomati. Further analysis of these non human homologous proteins predicted that 142 essential proteins were involved in unique metabolic pathways of C.trachomatis. The prediction of sub-cellular localization of the essential proteins was used to identify the membrane proteins which can be used as vaccine targets. There are 63 unique essential non-human homologous therapeutic targets found in the current study, which plays a vital role in the Peptidoglycan biosynthesis, Phosphotransferase system, Fatty acid biosynthesis and Bacterial secretion system of C.trachomatis.