Chlamydia trachomatis is a major cause of infectious blindness and sexually transmitted infection, with numbers of cases within Switzerland currently increasing. It is a bacterium with a complex lifecycle, requiring host cells for growth, which makes growth and manipulation in the laboratory non-trivial. Due to this, several novel techniques have had to be developed to allow access to the genomic information within clinical samples. Analysis of large, global collections of chlamydial genomes shows that the small, compact genome is subject to widespread recombination. This appears to be both an ancestral and ongoing phenomenon, with new genotypic combinations found recently in circulating populations throughout Europe and globally.