Symbiotic marine bacteria that are transmitted through the environment are susceptible to possible abiotic factors (salinity, temperature, physical barriers) that separates them from their hosts. Given that many symbioses are driven by host specificity, environmentally transmitted symbionts can alter symbiont preference depending on conditions over space and time. In order to determine whether the population structure of environmentally transmitted beneficial associations reflect host specificity or biogeography, we analyzed the genetic structure of Sepiola atlantica (Cephalopoda: Sepiolidae) and their Vibrio symbionts (V. fischeri and V. logei) in four Galician Rías (Spain). This geographical location is characterized by a jagged coastline with a deep-sea entrance into the land, ideal for testing whether such population barriers exist due to genetic isolation. We used haplotype estimates combined with nested clade analysis to determine the genetic relatedness for both S. atlantica and Vibrio bacteria. Analyses of molecular variance (AMOVA) were used to estimate variation within and between populations for both host and symbiont genetic data. Our analyses reveal a low percentage of variation among host populations, suggesting that these populations are panmictic, whereas between host population variation does exist due to geographical distance. In contrast, Vibrio symbionts are panmictic among and between populations, demonstrating that the hydrology of the rias are driving bacterial distribution (and not host specificity). Thus, for environmentally transmitted symbioses such as the sepiolid squid-Vibrio association, abiotic factors can be major selective force for determining population structure for one of the partners.