Lymphogranuloma venereum (LGV) is a chronic disease of the lymphatic system that is transmitted sexually and whose etiologic agents are L1, L2 and L3 serotypes of Chlamydia trachomatis. Since 2003 in Europe, USA, Canada and Australia have had outbreaks of L2 serotype infection that develops proctitis in place of LGV in men who have sex with men. It appears that these strains are a new genovariant of L2 serotype (L2b) that is developing a different pathology to LGV. However, the analysis of L2b genome not differs significantly to L2 genome (L2/434 UB) for which L2b is considered as a classic L2 strain. Despite this, new genovariantes of L2 and L2b are appearing, which develop or not LGV or proctitis so we need to do an analysis of its genome to identify genetic changes that these strains shown.