Pathogens can be influenced by the microbiome of their hosts. Therefore, characterizing the microbiome of hosts, particularly vectors, may help explain pathogen transmission patterns and facilitate the development of novel transmission-blocking approaches. Borrelia burgdorferi is a bacterium that is transmitted by blacklegged ticks (Ixodes scapularis) in the eastern and upper midwestern United States and causes Lyme disease in humans. Borrelia burgdorferi has been hypothesized to be susceptible to exclusion from the midgut of blacklegged ticks by other bacteria, however, blacklegged tick microbiomes have not been characterized across the entire geographic range of the tick. Here we compare the microbiomes of whole nymphal blacklegged ticks infected and uninfected with B. burgdorferi collected at three sites across the state of Delaware that have a high-incidence of Lyme disease. Infected and uninfected ticks did not differ in alpha diversity of their microbiomes and had similar microbiome compositions after removing B. burgdorferi from the analysis. Tick microbiomes varied among sampling locations in terms of both alpha and beta diversity, demonstrating that the tick microbiome can differ over small spatial scales. We also found at least one tick infected with the emerging pathogen B. miyamotoi. Further investigation of blacklegged tick microbiomes throughout their ranges and within specific tick tissues are needed to fully document the effect of microbiomes on B. burgdorferi infection in ticks.