Lyme disease is a serious health problem, with many patients requiring in-depth clinical assessment and extended treatment. In the present study, we provide the first records of the western blacklegged tick, Ixodes pacificus, and Ixodes spinipalpis parasitizing eastern cottontails, Sylvilagus floridanus. We also documented a triple co-infestation of 3 tick species (Ixodes angustus, I. pacificus, I. spinipalpis) feeding on an eastern cottontail. Notably, we discovered a unique member of the Lyme disease bacterium, Borrelia burgdorferi sensu lato (s.l.) in Canada. Ixodes spinipalpis ticks, which were collected from an eastern cottontail on Vancouver Island, British Columbia (BC), were positive for B. burgdorferi s.l. With the use of polymerase chain reaction amplification on the tick extracts and DNA sequencing on the borrelial amplicons, we detected Borrelia genomospecies 2, a novel subgroup of the B. burgdorferi s.l. complex. Based on 416 nucleotides of the flagellin B (flaB) gene, our amplicons are identical to the Borrelia genomospecies 2 type strain CA28. Borrelia genomospecies 2 is closely related genetically to other B. burgdorferi s.l. genospecies, namely Borrelia americana, Borrelia andersonii, and B. burgdorferi sensu stricto (s.s.) that cause Lyme disease. Like some other borrelial strains, Borrelia genomospecies 2 can be missed by current Lyme disease serology. Health-care providers must be aware that Borrelia genomospecies 2 is present in I. pacificus and I. spinipalpis ticks in far-western North America, and patients with clinical symptoms of Lyme disease need to be assessed for potential infection with this pathogen.