This study used nanopore sequencing technology to analyze the gut bacterial flora composition of Taiwanese cultured clams. Through an analysis of 12 gut microbiota samples of cultured clams from Cigu, Tainan, performed with the Epi2me platform, a total of 415,881 valid 16S sequences were successfully sequenced, and 314,348 of these sequences could be identified to the genus level. The 5 bacteria genera with the highest proportions in the clam gut bacterial flora were Vibrio, Mycoplasma, Endozoicomonas, Bacillus, and Anoxybacillus. The nanopore sequencing revealed greater taxonomic resolution than illumina sequencing platforms, and its slightly lower per read accuracy did not seem to affect the analysis very much. Both the software and hardware of nanopore sequencing technology is under continuous development, and its sequencing accuracy is also continuously increasing, meaning that the technology has great potential for gut bacterial flora analysis.