Abstract: The genomic information and transcriptome sequences of Batrachuperus yenyuanensis are rarely reported at present.In this study,the transcripts of this species were sequenced and assembled using Illumina HiSeq platform.A total of 36 252 unigenes were obtained through sequencing and assembling,with an average length of 937 bp and a N50 of 1 549 bp.Additionally,GC content,length distribution and expression level of unigenes were assessed.The result showed that the sequencing data was of high quality.Blasted against the Swiss-prot,Nr,Pfam,KEGG,KOG and GO,a total of 16 465,18 749,13 983,10 607,15 704 and 14 242 unigenes were annotated,respectively.According to the functional annotation results,17 472 coding sequence (CDS) were detected.A total of 2 779 microsatellite markers (SSR) and 3 100 single nucleotide polymorphisms (SNP) were identified.KEGG pathway analysis showed that 10 607 unigenes were annotated,and it was divided into 257 categories according to the different pathways.Among all the pathways,the number of unigenes involved in signal transduction pathway exhibited the largest proportion.In this study,the obtained transcriptome sequences provided rich data resources for further understanding of genetic diversity analysis,molecular marker development,population resource evaluation and conservation,as well as functional gene cloning of the B.yenyuanensis.