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Given the increasing challenges that Arctic cetaceans face, it is critical to investigate novel methods for assessing their health. Skin microbiomes have emerged as a promising method of detecting health issues that can help guide conservation efforts for free-ranging cetaceans. This study characterized the skin microbiome of 17 bowhead (BW) and 2 killer whales (KW). Fifty-six amplicon sequence variants were identified exclusively from cetacean samples, 20 belonged to BW, 13 to KW, and 23 to BW and KW. We identified bacteria from the genera Tenacibaculum and Psychrobacter, which have been previously described as bacteria that play a role in the health of cetaceans. In addition, in the healthy bowhead whale (H-BW) samples, we identified Clostridium sensu stricto 1 and 7, Carnobacterium spp., and Yersinia spp. which are of concern because these bacteria are opportunistic pathogens. Stranded BW had a less diverse microbiome than H-BW and had pathogens, including Aeromonas species and Streptococcus agalactia. Opportunistic pathogens of the genera Moritella (previously Vibrio spp.), Shewanella, Psychrilyobacter, and Legionella were discovered in KW. Due to their predator–prey relationships, the findings of this pilot study support the importance of keeping a close eye on the bowhead and killer whale populations in the Arctic.