The family Gastromyzontidae primarily inhabits mountainous streams in Southeast Asia. These fish have a flattened body shape， with broad paired fins， and in some species， the paired fins are specialized into a disc， enabling them to live in fast-flowing environments. To investigate the diversity and structure of the gut microbiota in Gastromyzontidae fish， MiSeq 16S rRNA high-throughput sequencing was conducted on gut samples from 12 species across eight genera， including Plesiomyzon baotingensis， Beaufortia pingi， Beaufortia kweichowensis， Liniparhomaloptera disparis， Erromyzon sinensis， Paraprotomyzon multifasciatus， Labidogastromyzon fangi， Labidogastromyzon changtingensis， Vanmanenia pingchowensis， Vanmanenia stenosoma， Vanmanenia homalocephala， and Formosania stigmata. The analysis focused on the number of operational taxonomic units （OTUs）， microbial community composition， Alpha diversity， and functional predictions. A total of 1，029 OTUs were identified， spanning 31 phyla， 75 classes， 173 orders， 278 families， 465 genera， and 689 species， with an average of 175 OTUs per sample and three shared OTUs. In terms of community composition， the dominant bacterial phyla were Proteobacteria， Fusobacteriota， Actinobacteriota， and Verrucomicrobiota， with Achromobacter，Cetobacterium， Plesiomonas，Mycobacterium being the dominant genera. The shared genera included Rhodococcus， Mycobacterium， and Leifsonia. Alpha diversity analysis revealed significant differences in species richness and diversity among the gut microbial communities of different fish species. Beaufortia pingi exhibited the highest diversity， while Vanmanenia stenosoma showed the lowest diversity. KEGG pathway analysis indicated that most genes encoded by the gut microbiota were related to metabolic processes， with pathways associated with amino acid transport and metabolism being the most abundant， accounting for 11.40%. From the perspective of OTU richness and PCoA analysis at the OTU level， it was difficult to predict associations between microbiotaand phylogeny. Compared with fish inhabiting plains and river-lake systems， the dominant genera in Gastromyzontidae fish included obligate aerobes such as Mycobacterium （9.47%）， as well as some facultative anaerobes that prefer aerobic environments， such as Achromobacter （24.91%）.