In Tasmania, Australia, the farmed Atlantic salmon (Salmo salmar L) industry utilizes marine leases to cultivate stock and faces opportunistic predation pressure from wild Australian fur seals (Arctocephalus pusillus doriferus). Microbial connectivity between aquaculture and wild pinnipeds was explored during this research, to find potential indicators for microbial sharing, identify potential pathogens at this interface, and elucidate potential effects of interactions on the microbiota of wild seals. High-throughput sequencing of the V1-V3 region of the 16S rRNA genes found in the gut microbial communities of 221 fur seals was performed; 41 males caught at fish farms, 50 fresh adult scats from haul-outs near farms, 24 necropsied seals, and controls from Bass strait rookeries including: 56 adult scats and 50 pup swabs. QIIME2 and R software were used for analysis of fur seal microbiomes, and to compare seal microbiomes to previously collected salmon microbiomes. Foraging at farms appears to shift biodiversity in fur seal microbiota; seals foraging at or near farms having greater phylogenetic diversity in their gut microbial communities compared to control seals. Taxonomic analysis showed a greater divergence in Proteobacteria representatives in male seals captured at farms compared to all other groups and identified indicator OTUs which could be used as minimally invasive indicators for interactions at this interface. These indicator OTUs included members of the following taxa: Clostridium sensu stricto I, Psychrobacter, Xanthomonadaceae, Suttonella, Pelomonas, an unclassified Weeksellaceae genus, Edwardsiella hoshinae, Pleisomonas shigelloides, and Cetobacterium ceti. Several potential pathogens were identified to monitor for human and animal health.