The establishment and maintenance of the light organ symbiosis between the Hawaiian bobtail squid Euprymna scolopes and the bioluminescent bacterium Vibrio fischeri depends on selection of V. fischeri and exclusion of non-symbiotic bacteria from the environment. Successful colonization of the host and cell-cell signaling between the partners triggers a morphogenetic program that leads to maturation of the association. Subsequent physical, biochemical and immunological mechanisms help to ensure that host-symbiont specificity is maintained. Current evidence suggests that the host’s cellular innate immune system, in the form of macrophage-like hemocytes, assists in mediating host tolerance of V. fischeri. To further understand the role of hemocytes in this association, we have used both transcriptomic and proteomic analyses of this cell type. We have identified a number of pattern receptors involved with the recognition of microbe-associated molecular patterns. Among these was a complete open reading frame to a novel peptidoglycan recognition protein (EsPGRP5) with conserved residues for predicted amidase activity. Other transcripts and proteins identified included members of the conserved NF-κB signaling pathway, predicted members of a complement-like pathway, the carbohydrate binding protein galectin and a putative cephalotoxin. Quantitative PCR of complement-like genes, cephalotoxin, EsPGRP5, and a nitric oxide synthase showed differential expression in circulating hemocytes isolated from adult squid with colonized light organs compared to those from cured hosts. These data suggest that light organ colonization influences gene expression of the cellular innate immune system of the host. Studies are currently underway to determine how hemocytes distinguish between V. fischeri and non-symbiotic bacteria in both juveniles and adults. In addition to the light organ symbiosis, female squid have, as part of their reproductive system, an accessory nidamental gland (ANG) that houses a bacterial consortium within epithelia-lined tubules. We have used a number of microscopy and molecular techniques to identify dominant members, including the Rhodobacterales (Phaeobacter spp.) and Verrucomicrobia. 16S rRNA fluorescent in situ hybridization revealed that many ANG tubules were dominated by specific bacterial taxa, such as Rhodobacterales, Verrucomicrobia or Cytophaga-Flavobacteria-Bacteroidetes. Our data also suggest that bacteria from the ANG are deposited directly into the jelly coat of freshly laid eggs. To begin to explore the function of the ANG bacterial consortium, we conducted a series of experiments whereby development of egg clutches (with and without antibiotic treatment) was monitored over a four-week period. Treated eggs developed a thick fungal biofilm that resulted in the death of the embryos. A fungal culture was isolated from this biofilm and morphological characterization and multi-locus sequence typing suggest that it is a haplotype of the Fusarium solani species complex, a group that includes pathogens of marine animals. Taken together, these data suggest ANG bacteria may protect developing squid embryos from fungal biofilms, similar to what has been described for bacterial egg protection of other marine invertebrates. Overall, E. scolopes offers the unique opportunity to study both a binary (light organ) and consortial (ANG) bacterial association in the same host.