Both deterministic and stochastic forces determine the representation and frequency of floral morphs in heterostylous plant populations. Phylogeographic analysis of molecular variation can provide information on the role of historical factors, including founder events, in affecting population morph structure. Here, we investigate geographical patterns of floral morph variation in a distylous shrub Luculia pinceana (Rubiaceae) by examining the relations between floral polymorphism and molecular (cpDNA and microsatellite) variation in 25 populations sampled throughout the distribution of the species in southwest China and adjacent countries. In 19 of the 25 populations, the frequency of floral morphs was not significantly different from the expected 1:1 ratio. The remaining populations were either L-morph biased (2) or monomorphic (4) for this form and were morphologically differentiated from the remaining populations in several floral traits, that is, corolla tube length, sex organ position and stigma-anther separation. Phylogeographic analysis supports the hypothesis that L. pinceana was initially split into west-central and eastern lineages in the Early Pleistocene (∼1.982 Mya). A centrally located lineage composed of morph-biased and monomorphic populations appears to have been subsequently derived from the west-central lineage, perhaps by a founder event after the last glacial maximum. Hypotheses to explain why these populations have not returned to equilibrium morph frequencies are considered.