The dataset includes two genome assemblies, HaplotypeA and HaplotypeB for the large-scale loach (Paramisgurnus dabryanus). HaplotypeB exhibits better completeness and has been uploaded to NCBI under the accession number [GCA_030506205.2]. Comprehensive annotations were performed for HaplotypeB, including the genome sequence file (HaplotypeB.fasta) and annotation files: HaplotypeB_gene.gff (gene annotation), HaplotypeB_pep.gff (protein annotation), and HaplotypeB_repeats.gff (repeat annotation). HaplotypeA.fasta is the genome sequence file for HaplotypeA, while HaplotypeA_gene.gff contains annotation data based on the annotations of HaplotypeB.fasta.