Abstract Although characterization of plant interactions has become a research hotspot to assess the adaptability of endangered plants, the underlying molecular basis remains elusive. Dove tree (Davidia involucrata) seedlings were watered with distilled water (CK), leaf water extract (0.025 g mL−1) and branch water extract (0.1 g mL−1) from Cornus controversa, respectively. Subsequently, the morphology, biomass and gene expression levels of DiSOC1-b and DiCCoAOMT1 were analyzed. The results showed that morphological traits and biomass accumulation of D. involucrata seedlings were decreased by the addition of leaf water extracts, and increased by branch water extracts. Moreover, the gene expression level of DiSOC1-b was significantly down-regulated, while the gene expression level of DiCCoAOMT1 was significantly up-regulated in the stems and roots of D. involucrata upon treatment with leaf water extracts of C. controversa. In contrast, the gene expression level of DiSOC1-b was significantly up-regulated in the leaves and stems, while the gene expression level of DiCCoAOMT1 was significantly down-regulated in the roots of D. involucrata upon treatment with branch water extracts of C. controversa. In addition, the expression level of DiSOC1-b was positively correlated with most of morphological traits and total biomass (P < 0.05), while DiCCoAOMT1 was negatively correlated with the majority of morphological traits in D. involucrata seedlings (P < 0.05). Taken together, these results suggest that water extracts from the leaves and branches of the C. controversa exhibit opposite allelopathic effects and affect the expression levels of genes related to growth (DiSOC1-b) and environmental adaptability (DiCCoAOMT1) in D. involucrata seedlings.