Rickettsiae are small, gram negative, rod-shaped, obligate intracellular, endosymbiotic alphaproteobacteria that are responsible for several of the oldest zoonoses known to man. Over the past 10 years, genetic analysis of rickettsiae found in arthropod vectors, mammal reservoirs and clinical disease specimens has resulted in the recognition of new pathogenic rickettsial species and a re-evaluation of disease caused by species previously thought to be non-pathogenic, including, most recently Rickettsia philipii strain 364D. Interference between different Rickettsia species coinfecting ticks has been described, although, the mechanisms are unknown. Interference is thought to lead to dramatic epidemiological consequences such as defining the geographic distribution of disease. In this dissertation, the association and possible interference between Rickettsia spp. and other bacteria were investigated using two different invertebrate models, namely, insect flea beetles of the Longitarsus genus and the arachnid tick Dermacentor occidentalis. Longitarsus flea beetles are herbivorous and complete their entire life cycle on and around an individual plant and its soil, in contrast to Dermacentor ticks that imbibe blood from three different vertebrate hosts to complete their life cycle. PCR amplification and Sanger sequencing of partial rickettsial ompA and IGR genes and PCR of 16S rRNA gene sequences followed by next generation sequencing, respectively, were used to identify rickettsias and other bacteria that constituted the microbiome of these invertebrate hosts. The Quantitative Insights Into Microbial Ecology (QIIME) open source bioinformatics pipeline was used for sequence data analysis and to explore the different intermicrobial and microbe-host relationships of Rickettsia. We found that while the species of Longitarsus was related to the make-up of their Rickettsia and Wolbachia endosymbionts, in contrast, in Dermacentor ticks, other Francisella-like endosymbionts and, to a lesser extent, non-endosymbiotic organisms appeared to “interfere” with rickettsial infection. An additional goal of this investigation was to describe the prevalence and distribution of Rickettsias in Dermacentor occidentalis in San Diego County. Both pathogenic and nonpathogenic Rickettsias were detected in ticks collected from different locations over several years. These findings are described in the dissertation that follows.