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.