Borrelia burgdorferi sensu lato is the causative agent of Lyme disease, which afflicts both humans and some domestic animals. B. burgdorferi, a highly evolved extracellular pathogen, uses several strategies to survive in a complex enzootic cycle involving a diverse range of hosts. This review focuses on the unique adaptive features of B. burgdorferi, which are central to establishing a successful spirochetal infection within arthropod and vertebrate hosts. We also discuss the regulatory mechanisms linked with the development of molecular adaptation of spirochetes within different host environments.