Two East Asian finless porpoises (Neophocaena asiaeorientalis sunameri) in Ningbo, East China Sea, China, were observed to be bacterially infected between the fat layer and muscle layer. The microbial communities in pus samples were identified by metagenome sequencing 16S in the PacBio platform and explored the relationship between emaciation and bacterial infection. The present paper was the first report on bacterial diversity in infected tissue pus of finless porpoise. In total, 101 bacterial species were identified, and the top nine species were Rhodococcus qingshengii (26.25%), Rhodococcus jialingiae (22.43%), Ralstonia pickettii (16.03%), Moraxella osloensis (9.97%), Psychrobacter cibarius (2.97%), Flavobacterium johnsoniae (2.11%), Flavobacterium chungbukense (1.80%), Stenotrophomonas maltophilia (1.73%) and Serratia marcescens (1.62%). These main bacteria could cause various diseases or metabolic disorder, such as endocarditis, meningitis, bacteraemia, septicaemia, and so on; they also involve microbiome metabolism of amino acids (12.47%), carbohydrates (11.58%), xenobiotic biodegradation (7.81%), lipids (6.01%) and energy (4.98%). Regardless of the type of disease metabolic disorder will firstly cause body weight loss. In conclusion, these bacteria could cause diseases or metabolic disorders, resulting in emaciation of East Asian finless porpoises. Admittedly, pathogenic assay is furthermore needed to determine the mechanisms regarding the pathological phenomena.