To attain genomic infromation of hybrid snakehead, the transcripts of hybrid snakehead were collected using high-throughput sequencing and subject to the transcriptomic analysis. A total 52 065 unigenes were generated by de novo assembly with base length ranging from 201 bp to 12 407 bp in length and the average length 710 bp. Unigenes qualities for several aspects were assessed, such as length distribution, GC content and expression level. The sequencing data was of high quality. Further analysis of data showed that 20 535 coding sequence(CDS) and 37 324 single nucleotide polymorphisms(SNP) and 7 830 microsatellite markers(SSR) were in transcriptome data. With blast the results against 6 available databases(Swiss-Prot, Nr, Pfam, KEGG, KOG and GO), a total of 20 955, 28 938, 19 339, 14 052, 19 358 and 18 635 unigenes were annotation, respectively. Based on the results of comparative analysis with the GO functional database, all unigenes could be annotated into three categories including biological processes, cellular components and molecular function. The three categories could be further subdivided to 50 groups. KEGG metabolic pathways analysis indicated that the unigenes could be divided into 5 categories that can be further grouped into 30 subgroups and 268 pathways, with the signal transduction pathway having the most unigenes, 1 716 unigenes.