Mammalian gastrointestinal (GI) tract microbial communities are critical for host health. However, the microbiota along the GI tract in cetaceans has not been well characterized compared to other animals. In this study, the bacteria and fungi present in the stomach, foregut, hindgut and feces, of East Asian finless porpoises (Neophocaena asiaeorientalis sunameri, EAFPs) were characterized using high-throughput sequencing analysis. The bacterial and fungal diversity and richness in the stomach, hindgut and fecal samples tended to be higher than those in the foregut. Bacterial taxonomic compositions found in the hindgut and feces were different from those seen in the stomach and foregut. A greater proportion of strict anaerobic bacteria including Clostridia, Fusobacteria, and Ruminococcaceae were found in the hindgut and fecal samples. The fungal communities present in stomach samples differed from those detected in other regions to some extent. Zygomycota and Neocallimastigomycota were more predominant in the stomach. Some potential pathogens, such as Helicobacter spp. and Vibrio spp., were commonly present along the GI tract. Our study confirms that the fecal microbiota can represent the whole GI tract to some extent because of their relatively higher microbial diversity and presence of potential pathogens. Our study provides the first comprehensive characterization of the EAFPs GI microbiota, expanding on the current knowledge about the bacterial diversity in the GI tract of cetaceans. In addition, this is the first study characterizing the fungal diversity of any species of porpoise.