Comparative analyses of the genetic differentiation in microsatellite markers (FST) and leaf morphology characters (QST) of Amphicarpaea edgeworthii Benth. were conducted to gain insight into the roles of random processes and natural selection in the population divergence. Simple sequence repeat analyses on 498 individuals of 19 natural populations demonstrate that a significant genetic differentiation occurs among populations (mean FST = 0.578), and A. edgeworthii is a highly self-fertilized species (mean selfing rate s = 0.989). The distribution pattern of genetic diversity in this species shows that central populations possess high genetic diversity (e.g. population WL with HE = 0.673 and population JG with HE = 0.663), whereas peripheral ones have a low HE as in population JD (0.011). The morphological divergence of leaf shape was estimated by the elliptical Fourier analysis on the data from 11 natural and four common garden populations. Leaf morphology analyses indicate the morphological divergence does not show strong correlation with the genetic differentiation (R = 0.260, P = 0.069). By comparing the 95% confidence interval of QST with that of FST, QST values for five out of 12 quantitative traits are significantly higher than the average FST value over eight microsatellite loci. The comparison of FST and QST suggests that two kinds of traits can be driven by different evolutionary forces, and the population divergence in leaf morphology is shaped by local selections. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 505–516.