Amplified fragment length polymorphism (AFLP) fingerprint was the measure used to reveal the patterns of genetic variation within the Spiraea japonica L. f. complex, in the context of physical environment differentiation stemming from the Himalaya–Tibet plateau uplift, the most significant geological event in eastern Asia since the late Paleocene. The complex displays obvious genetic heterogeneity among geographic populations, which was greater in south-western China than in eastern China. The uplift of the Himalaya–Tibet plateau, and consequent increase in environmental complexity in south-western China, is presumed to be responsible for this genetic structure. The obvious genetic heterogeneity among populations or varieties of the S. japonica complex indicates that the rich biodiversity in south-western China is possibly based on genetic variation, suggesting that the biodiversity centre of south-western China represents a tremendous gene pool. It also supports the idea that the protected area and conservation investment made in south-western China should be further augmented. In addition, the greater genetic heterogeneity displayed by plants in south-western China suggests that conservation plans in this region should be more inclusive than those in eastern China.