A potential role of seabirds in spreading Lyme disease (LB) spirochetes over large spatial scales was suggested more than 10 years ago when Borrelia garinii was observed in marine birds of both hemispheres. Since then, there have been few studies examining the diversity of Borrelia spp. circulating in seabirds, or the potential interaction between terrestrial and marine disease cycles. To explore these aspects, we tested 402 Ixodes uriae ticks collected from five colonial seabird species by amplification of the flaB gene. Both the average prevalence (26.0%+/-3.9) and diversity of LB spirochetes was high. Phylogenetic analyses grouped marine isolates in two main clades: one associated with B. garinii and another with B. lusitaniae, a genospecies typically associated with lizards. One sequence also clustered most closely with B. burgdorferi sensu stricto. Prevalence in ticks varied both among seabird species within colonies and among colonies. However, there was no clear association between different Borrelia isolates and a given seabird host species. Our findings indicate that LB spirochetes circulating in the marine system are more diverse than previously described and support the hypothesis that seabirds may be an important component in the global epidemiology and evolution of Lyme disease. Future work should help determine the extent to which isolates are shared between marine and terrestrial systems.