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The gut microbiome is a unique marker for cetaceans’ health status, and the microbiome composition of their skin wounds can indicate a potential infection from their habitat. Our study provides the first comparative analysis of the microbial communities from gut regions and skin wounds of an individual Indo-Pacific finless porpoise (<i>Neophocaena phocaenoides</i>). Microbial richness increased from the foregut to the hindgut with variation in the composition of microbes. <i>Fusobacteria</i> (67.51% ± 5.10%), <i>Firmicutes</i> (22.00% ± 2.60%), and <i>Proteobacteria</i> (10.47% ± 5.49%) were the dominant phyla in the gastrointestinal tract, while Proteobacteria (76.11% ± 0.54%), <i>Firmicutes</i> (22.00% ± 2.60%), and <i>Bacteroidetes</i> (10.13% ± 0.49%) were the dominant phyla in the skin wounds. The genera <i>Photobacterium</i>, <i>Actinobacillus</i>, <i>Vibrio</i>, <i>Erysipelothrix</i>, <i>Tenacibaculum</i>, and <i>Psychrobacter</i>, considered potential pathogens for mammals, were identified in the gut and skin wounds of the stranded Indo-Pacific finless porpoise. A comparison of the gut microbiome in the Indo-Pacific finless porpoise and other cetaceans revealed a possible species-specific gut microbiome in the Indo-Pacific finless porpoise. There was a significant difference between the skin wound microbiomes in terrestrial and marine mammals, probably due to habitat-specific differences. Our results show potential species specificity in the microbiome structure and a potential threat posed by environmental pathogens to cetaceans.