Phosphites have been used in the control of sudden oak death, however, the precise mode of action of these compounds is not fully understood. We designed an inoculation experiment on four open-pollinated tanoak families, previously defined as partially resistant. Stems of treatment-individuals were sprayed with phosphite, and 7 days later distal leaves were inoculated with the sudden oak death pathogen Phytophthora ramorum. Leaves from treated and untreated control plants were harvested for RNA extraction before and seven days after inoculation, and transcriptomes of both host and pathogen were analyzed. We found that sets of genes associated with innate resistance and with phosphite-induced resistance largely overlapped within a more susceptible but phosphite-treatment responsive tanoak family, supporting the hypothesis that phosphite treatment increases the resistance of susceptible host plants to Phytophthora infection. In addition, we found that genes of the pathogen involved in detoxification, such as ATP-binding cassette (ABC) transporters and vitamin B₆ biosynthesis genes, were upregulated in phosphite-treated plants, but not in untreated plants. In summary, our dual RNA-Seq supports a dual mode of action of phosphite compounds, including a direct toxic effect on P. ramorum and an indirect enhancement of resistance in the tanoak host.