Veronica hederifolia (Plantaginaceae) — an invasive, alien weed in eastern China — is of great concern due to its potential to spread. This study was conducted to determine the genetic diversity of V. hederifolia in comparison with several congeneric species, including V. persica, V. arvensis, V. didyma and V. peregrina as outgroups, using the Amplified Fragment Length Polymorphism (AFLP) technique. The samples of V. hederifolia were collected from 24 locations in Nanjing and Zhoushan, and genomic DNA was digested with the enzymes EcoRI/MseI and amplified with six E 3/M 3 primer combinations. Both mono- and polymorphic AFLP markers were analyzed to estimate genetic diversity of V. hederifolia based on a range of standard indicators. A high percentage of polymorphic bands (89.23%) existed in the populations examined, implying high genetic diversity. Based on all genetic indices, the Nanjing population, which was the first reported in China, exhibited greater genetic diversity than the Zhoushan population. Substantial variation was also found among individual plants collected from a single site near Nanjing, with 79.56% polymorphism. This high genetic diversity indicates this weed species potentially has broad adaptability. Cluster analysis of AFLP data placed V. hederifolia samples into three groups depending largely on geographical locations.