The white perch Morone americana is a commercially and recreationally important species found in coastal waters of eastern United States. Despite its wide geographic distribution and economic importance, genomic resources for understanding population structure are limited. In this study, we applied double digest restriction site-associated DNA sequencing technique to develop SNP markers and investigate the population structure of M. americana sampled from four geographical regions in Delaware Bay and Chesapeake Bay, USA. We identified 621 putatively neutral SNPs by applying a stringent filtering procedure. Based on these SNP markers, population structure inferences were conducted for the four populations. This study provides a valuable resource for further research on genetic structure and demographic history of M. americana.