As part of the Western Forest Transcriptome Survey, we used Massively Parallel Sequencing to concurrently sequence the transcriptomes of a generalist invasive pathogen (Phytophthora ramorum) and its most susceptible California Floristic Province native host (tanoak, Notholithocarpus densiflorus) during the course of their interaction. We analyzed 43.5 Mbp of sequence from 4 experimental conditions, of which 18.8 Mbp mapped to the P. ramorum genome sequence. We report on the characterization of the P. ramorum genes found to be active during infection, the assembly of a de novo reference transcriptome for tanoak, and the characterization of tanoak gene regions differentially expressed after infection, including regions associated with pathogenicity and resistance. These findings are an important step in understanding the genetics of interactions of forest hosts and their pathogens. Pathogen introductions can quickly have devastating effects on species and ecosystems, but developing the breeding populations used in traditional forest genetics is a decades-long undertaking. The application of genomic methods to novel host-plant interactions will ultimately allow a much faster response to a present ecological threat.