This review summarizes the transcendental changes that have recently occurred in the taxonomy of the bacteria known as Chlamydia, the clinical importance of the new species, and its identification procedures. The new classification of the order Chlamydiales is based on phenotypic and antigenic properties, on the host range and on the phylogenetic analysis of the ribosomal operon, and provides a reliable procedure for the identification of current species and the establishment of new taxa. Chlamydiales are important human and animal pathogens. Its ability to produce respiratory tract infections among other clinical presentations is a frequent finding of the organisms, being present in Chlamydophila pneumoniae, Chlamydophila psittaci, Chlamydia trachomatis, and in the recent described families Simkaniaceae and Parachlamydiaceae. Chlamydiales are the unique exclusive intracelular bacteria of eukaryotic cells. The description of the family Parachlamydiaceae, genera Parachlamydia and Neochlamydia, both endosymbionts of free living amoeba, highlights the phylogenetic diversity of the order, and suggests a greater environmental reservoir.