Chlamydiae is a bacterial phylum of obligate endosymbionts of eukaryotes that includes notorious animal pathogens, such as Chlamydia trachomatis, but also symbionts of microbial eukaryotes. Studying this group has wide evolutionary relevance, from the evolution of symbioses and pathogenesis, to eukaryote evolution. Using metagenome-resolved genomics, we have recently expanded genomic diversity within the phylum. Chlamydiae have previously been implicated in the evolution of primary plastid-bearing eukaryotes, which include algae and plants. Using recently expanded chlamydial genomic diversity, work is ongoing to systematically re-assess chlamydial genetic contributions through horizontal gene transfer during this event, and more generally throughout eukaryotic evolution.