D. occidentalis is one of the most common tick species found in San Diego and is a vector of human pathogens including Francisella tularensis and Rickettsia philipii. This is the first study of the microbiome of D. occidentalis ticks using NGS technologies to examine pathogen interference within the tick microbiome. Although Francisella tularensis has been detected previously in ticks in San Diego (Kugeler et al., 2005), none of the ticks harbored this bacterium or genera of other recognized zoonotic tick-borne pathogens such as Borrelia, Anaplasma, Ehrlichia, Babesia or Bartonella; however, a low percentage of the ticks were infected with spotted fever group Rickettsia: 2.5% with R. philipii and 8.2% with R. rhipicephali. This is a slightly lower prevalence of R. philipii than surveys of ticks performed in Orange, Riverside, Los Angeles, Santa Barbara and Ventura counties north of San Diego, that reported an overall 7.5% prevalence of R. philipii (Wikswo et al., 2008) but is within the range of R. philipii prevalence reported from northern California of 0.4–5.1% (Lane et al., 1981; Philip, Lane & Casper, 1981). Similar to other tick species, the microbiome of D. occidentalis was dominated by Proteobacteria, primarily Rickettsia or Francisella, with lesser amounts of Sphingomonas, Methylobacterium and Hymenobacter (Bacteroidetes). These last three genera are all decomposer microbes found in the soil and except for Hymenobacter, have been detected in other tick microbiome studies. Even though the ticks were washed multiple times before DNA extraction, the possibility that some of these represent surface bacteria cannot be completely excluded. Although not performed in this study, removal of any OTUs detected by sequencing a sterile water negative control would also improve the sequence quality of future analyses. However, it is worth noting that members of the genus Sphingomonas were also found in two different studies of Ixodes tickes (Van Treuren et al., 2015), including one that studied larvae, suggesting that this genus may be arthropod-associated.