We study the mutualistic association between the Hawaiian bobtail squid Euprymna scolopes and the bioluminescent bacterium Vibrio fischeri. While the molecular conversation between partners has been partially elucidated over the initiation of the symbiosis (Chun et al. 2008 Kremer et al. 2013), the influence of symbiosis gene expression in the more mature association has not been explored yet. As the rearing of squid in controlled symbiotic conditions is now possible (Koch et al. 2013), this studies aims at answering the following questions: (i) how does persistent colonization affect gene expression of adult light organ tissues, and how do these patterns compare to the transient initial infection by the ?lux mutant of V. fischeri? (ii) which biological functions are influenced by symbiosis and how do they participate in production of a niche where symbionts thrive and in the tolerance of the symbiont? Using next-generation sequencing (Illumina technology, 2x100bp), we compared whole light-organ gene expression of 4-week old squid uninfected by V. fischeri (Aposymbiotic), infected by wild type V. fischeri (WT), or by a mutant strain defective in light production and that do not persist in the light organ (?lux).