Ticks are the primary arthropod vectors of human pathogens in North America and Europe. The lone star tick, Amblyomma americanum, is a competent vector of various pathogenic microorganisms, and it is expanding its geographic distribution into the Midwest and Northeast regions of the United States. Little is known about how genomic diversity or microbial diversity affect the ability of specific pathogens to infect a tick. The main objective of our research is to generate an integrated genetic epidemiology for tick-borne diseases that incorporates the genomic diversity of vector, the species diversity of its microbiome, and its load of known pathogens. Our hypothesis is thatgenomic diversity of tick vectors is positively associated with microbial species diversity and negatively associated with pathogen load. To characterize the diversity and composition of the microbiome, we used Illumina sequencing of the 16S rRNA bacterial gene. Specifically, we examined differences in microbial community structure and metabolic pathways between two regions at the boundary of the lone star tick’s expanding range, between sexes, and between wild and laboratory-reared tick populations. To characterize genomic diversity of the tick vector, we used Restriction site-Associated DNA sequencing (RAD-seq) to discover and genotype thousands of SNPs. Finally, to measure the pathogen loads of ticks, we are using Nanopore sequencing to obtain long reads and identify specific strains of Rickettsia, Ehrlichia, and Borrelia. The microbiome analyses reveal that geographic region and sex strongly influence alpha diversity, beta diversity, the relative abundance of particular taxa, and the prevalence of pathogens. Additionally, distinct taxonomic profiles of the tick microbiome lead to distinct functional profiles between the sexes, highlighting important vitamin and heme metabolic pathways that are significantly more abundant in the metagenomes of female ticks. RAD-seq generated a total of 4.7 billion reads that mapped to the Amblyomma americanum reference genome and yielded an average of 50,574 SNPs per tick sample. We are investigating the spatial distribution of this genomic variation among populations of lone star tick near the western and northern species range boundaries. We are also just beginning to examine the effects of genomic diversity and microbial diversity on pathogen infection in individual ticks.