Borrelia burgdorferi sensu lato (s.l.) forms a diverse group of tick-borne spirochetes that includes the agents of Lyme borreliosis. The various genospecies and genotypes of B. burgdorferi s.l. mainly occur in temperate climates of the Northern hemisphere. The spirochetes are maintained in complex transmission webs involving many vertebrate hosts, but only a few hard tick species of the Ixodes ricinus/persulcatus species complex. Here, we demonstrate that B. burgdorferi s.l. represents a metapopulation of different ecological populations that are host-associated. We present a biological model of spirochete transmission through ticks and hosts that explains the variable fitness of Borrelia strains in different ecological niches. We conclude that multiple niche polymorphism maintains the genetic diversity of B. burgdorferi s.l. in the environment.