Summary The marine bacterium Vibrio fischeri is the monospecific symbiont of the Hawaiian bobtail squid, Euprymna scolopes , and the establishment of this association involves a number of signaling pathways and transcriptional responses between both partners. We report here the first full RNA‐Seq dataset representing host‐associated V. fischeri cells from colonized juvenile E. scolopes , as well as comparative transcriptomes u...