Two living organisms of A. brama were purchased from local fisherman lived in BeiTun town located in the midstream of the Irtysh River. These samples were collected from the Irtysh River basin and suitable for the identification of molecular markers for subsequent ecological analyses. The other two individuals were collected using gill nets from downstream (near Kazakhstan) of the Irtysh River in China. Sequencing was performed on an Illumina Hiseq 2000 platform and millions of 125bp paired-end reads were generated.