The genusChlamydiacontains important obligate intracellular bacterial pathogens to humans and animals, includingC. trachomatisandC. pneumoniae. Since 1998, when the firstChlamydiagenome was published, our understanding of how these microbes interact, evolved and adapted to different intracellular host environments has been transformed due to the expansion of chlamydial genomes. This review explores the current state of knowledge inChlamydiagenomics and how whole genome sequencing has revolutionised our understanding ofChlamydiavirulence, evolution, and phylogeny over the past two and a half decades. This review will also highlight developments in multi-omics and other approaches that have complemented whole genome sequencing to advance knowledge ofChlamydiapathogenesis and future directions for chlamydial genomics.