Strain diversity in host-microbe symbioses represents an opportunity for genetic diversity to impact the relationship. In order to determine the strain diversity of V. fischeri associated with a wild-caught, adult, E. scolopes squid, a bioinformatic approach comparing the genomes of 12 strains isolated from the squid identified three distinct genetic groups of strains associated with the host. Identification of these groups presents an opportunity to study the ways individual strains interact within the symbiosis further.