Background: Chlamydia suis is an endemic pig pathogen, belonging to a fascinating genus of obligate intracellular pathogens. Of particular interest, this is the only chlamydial species have naturally acquired genes encoding for antibiotic resistance. To date the distribution and mobility of the Tet-island is not well understood. Our study focused on whole genome sequencing of C. suis isolates from a recent porcine cohort within Switzerland, combined with data from USA tetracycline-resistant isolates.Results: The genome of C. suis has unprecedented diversity and shows a high rate of recombination. Very distinct strains circulate within Europe, and even within individual Swiss farms, whereas New World isolates have more restricted diversity and appear to derive from European isolates. There are several possibilities as to the origins of the Tet-island within C. suis, with recombination a major factor in its transmission. The architecture of the Tet-island is variable, but the tetA(C) gene is always intact. Selective pressure from tetracycline use within pigs leads to a higher number of Tet-island carrying isolates, which tend to be lost in the absence of such pressure.Conclusions: C. suis has a very plastic genome, highly affected by recombination and plasmid exchange. A large diversity of isolates are found circulating in Swiss farms, suggesting that C. suis originated around Europe and historical strain transfers to the USA have occurred. Under antibiotic pressure, strain replacement occurs rather than loss or gain of the Tet-island. The Tet-island appears to be a recent import into the genome of C.suis, with an American origin possible.