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The bacteria in the Streptococcus bovis/equinus complex (SBEC) and Streptococcus phocae have caused significant morbidity and mortality in northern sea otters (Enhydra lutris kenyoni). In order to illuminate the persistence and possible mechanisms of transmission of SBEC and S. phocae, the presence and absence of these bacteria were compared with 31 habitat attributes in Kachemak Bay and Resurrection Bay, Alaska. Bay mussels or water were collected at 1600‐m intervals around the perimeters of each bay and habitat attributes were recorded onsite and/or determined using ShoreZone. PCR was used to confirm the presence of bacteria, and presence was correlated with habitat attributes. Geographic spatial analysis revealed a cluster of low occurrence of both SBEC and S. phocae in an extremely shallow portion of Kachemak Bay that may be due to drying of the area between tide cycles. A cluster of high occurrence of S. phocae on the northeast side of the Kachemak Bay was identified that may be associated with harbor seal presence. No statistically significant clusters were found in Resurrection Bay. Habitat attributes (rockweed, eelgrass, habitat class, soft brown kelp and substrates of rock, sand and boulder) were found to be associated with presence of the target bacteria; however, relationships were not consistent with the bacteria or each bay. This could be due to the complexity of the relationship between SBEC and S. phocae and their environments, as well as intrinsic differences (such as nearshore temperatures) between Kachemak and Resurrection Bays. [ABSTRACT FROM AUTHOR]