Chlamydia trachomatis, one species ofChlamydiaspp., has the greatest impact on human health and is the main cause of bacterial sexually transmitted diseases and preventable blindness among allChamydiaspp. species. The obligate intracellular parasitism and unique biphasic developmental cycle ofC. trachomatisare the main barriers for the development of tools of genetic manipulation. The past decade has witnessed significant gains in genetic manipulation ofC. trachomatis, including chemical mutagenesis, group II intron-based targeted gene knockout, fluorescence-reported allelic exchange mutagenesis (FRAEM), CRISPR interference (CRISPRi) and the recently developed transposon mutagenesis. In this review, we discuss the current status of genetic manipulations ofC. trachomatisand highlights new challenges in the nascent field ofChlamydiagenetics.