Chlamydiaceaeare obligate intracellular Gram-negative bacteria found all over the world and known to cause various forms of disease in animals and humans. Urban pigeons are known to be an important reservoir ofChlamydia psittaci, the agent of human psittacosis. In this study, we examined the influence of pigeon houses used to regulate pigeon populations and of melanin-based coloration on several epidemiological parameters ofChlamydiaceaein 708 urban pigeons in Paris. We also identified species and genotypes ofChlamydiaceaepresent in Parisian populations. First, our results revealed that pigeons roosting and breeding in pigeon houses were equally infected byChlamydiaceaeas those that did not. Second, we found that dark melanic pigeons excreted moreChlamydiaceaethan pale melanic ones. Finally, species and strain diversities were very low: all samples were ofC. psittacigenotype B. Nevertheless, two atypicalChlamydiaceaewere identified based on 16S rRNA andompA sequences. Our study thus highlights the importance of considering environmental and host phenotype when investigating the epidemiology of infectious diseases.