Female Hawaiian bobtail squid, Euprymna scolopes, harbor a symbiotic bacterial community in a reproductive organ, the accessory nidamental gland (ANG). This community is known to be stable over several generations of wild-caught bobtail squid but has, to date, only been examined for one population in Maunalua Bay, Oahu, Hawaii. This study assessed the ANG and corresponding egg jelly coat (JC) bacterial communities for another genetically isolated host population from Kaneohe Bay, Oahu, Hawaii using 16S amplicon sequencing. The bacterial communities from the ANGs and JCs of both populations were found to be similar in richness, evenness, phylogenetic diversity, and overall community composition. However, the Kaneohe Bay samples formed their own subset within the Maunalua Bay ANG/JC community. An Alteromonadaceae genus, BD2-13, was significantly higher in relative abundance in the Kaneohe Bay population, and several Alphaproteobacteria taxa also shifted in relative abundance between the two groups. This variation could be due to local adaptation to differing environmental challenges, to localized variability, or to functional redundancy among the ANG taxa. The overall stability of the community between the populations further supports a crucial functional role that has been hypothesized for this symbiosis.