Rutilus rutilus (roach) is native to most of Europe and western Asia, and the Irtysh River basin in Sinkiang, northwest Chinais the marginal area of their natural distribution. The wide distribution and unique characteristic of this species makes it anideal model for analysing ecological and comparative genomics. However, the limited genome sequences available for thisspecies have hindered these investigations. Transcriptomes from the brains and livers of five individuals collected from theIrtysh River basin were sequenced using Illumina paired-end sequencing technology. A collection of 132,289 unigenes for thisspecies were obtained using a de novo assembly method based on nearly 120 million clean reads encompassing more than 14Gb data. Approximately 37.5% (49,656), 27.1% (35,867) and 21.2% (27,987) of the transcriptome had homologues depositedin Nt, Nr and Swiss-Prot, respectively; 12.3% (16,328) were assigned to eukaryotic orthologous groups of proteins classifi-cations, and 21.5% (28,429) harboured Interpro domains. On the basis of the assembled transcriptome, we detected 177,493single-nucleotide variation resident in 39.3% (52,029) of the sequences and 20.8% (27,497) of the sequences harbouring 36,639simple sequence repeats. The identified molecular markers are a basis for further ecological analysis, and the transcriptome repor-ted here allows for more extensive evolutionary analyses of the Cyprinidae, the most species-rich family of freshwater fishes.