Anthozoans are a class of Cnidarians that includes scleractinian corals, anemones and their relatives. Despite a global rise in disease epizootics impacting scleractinian corals, little is known about the immune response of this key group of invertebrates. To better characterize the anthozoan immune response, we used the model anemone Exaiptasia pallida to explore the genetic links between the anthozoan-algal symbioses and immunity in a two-factor RNA-Seq experiment using both symbiotic and aposymbiotic(menthol-bleached) Exaiptasia pallida exposed to the bacterial pathogen Vibrio coralliilyticus. Multivariate and univariate analyses of Exaiptasia gene expression demonstrated that exposure to live Vibrio coralliilyticus had strong and significant impacts on transcriptome-wide gene expression for both symbiotic and aposymbiotic anemones, but we did not observe strong interactions between symbiotic state and Vibrio exposure. There were 4,164 significantly differentially expressed (DE) genes for Vibrio exposure, 1,114 DE genes for aposymbiosis, and 472 DE genes for the additive combinations of Vibrio and aposymbiosis. KEGG enrichment analyses identified 11 pathways - involved in immunity (5), transport and catabolism (4) and cell growth and death (2) - that were enriched due to both Vibrio and/or aposymbiosis. Immune pathways showing strongest differential expression included complement, coagulation, nucleotide-binding and oligomerization domain (NOD), and Toll for Vibrio exposure and coagulation and apoptosis for aposymbiosis.