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The white back planthopper (WBPH), Sogatella furcifera (Horváth) (Hemiptera: Delphacidae), is an important destructive rice pest in Asia that has caused serious economic losses in the main rice‐producing areas of China. To effectively manage this rice pest, it is necessary to investigate its genetic variation and genetic structure and speculate the migration route in China. In this study, we used 12 nuclear microsatellite loci to analyse the genetic variation, gene flow and genetic structure of WBPH in 25 geographic populations in China. Overall, high levels of genetic diversity and genetic differentiation among most populations were detected. Neighbour‐joining dendrograms, STRUCTURE and principal coordinate analysis (PCoA) revealed three genetically distinct groups and exhibited an admixed phylogeographic structure. There was a significant low positive correlation between genetic and geographic distances (r2 = 0.105, p = 0.001), which indicated the role of geographic isolation in the genetic structure of WBPH. Migrant routes detection indicated frequent gene flow exchange between North China and Central China, and low bidirectional gene flows between Northeast China and other regions were detected. Accordingly, this study provides useful data for resolving the genetic relationships and large‐scale migration route of the WBPH and thus contributes to developing more effective management strategies for controlling this pest. [ABSTRACT FROM AUTHOR]