Recently, a new method of sequencing called next generation sequencing has been widely applied due to its lower cost per sequencing output compared to traditional sequencing technologies. Genomic regions of Pacific white shrimp have been selected to construct materials for sequencing using the Illumina Solexa technology. We then used de novo techniques to assemble the sequences into 8,007 contigs, and identified ~ 256K genetic markers. Due to the potential complex genome structure of Pacific white shrimp, we had a success rate of validating about 2/3 of the genetic markers chosen. This important resource could be used for the improvement of growth rate and disease resistance by the shrimp industry