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Background  It has been recognized that a certain amount of habitat disturbance is a facilitating factor for the occurrence of natural hybridization, yet to date we are unaware of any studies exploring hybridization and reproductive barriers in those plants preferentially occupying disturbed habitats.  Buddleja  plants (also called butterfly bush) generally do grow in disturbed habitats, and several species with hybrid origin have been proposed, based solely on morphological evidence.    Results  In the present study, we test the hypothesis that  B. × wardii  is of natural hybridization origin in two sympatric populations of three taxa including  B. × wardii  and its parents ( B. alternifolia  and  B. crispa ) plus 4 referenced parental populations, using four nuclear genes and three chloroplast intergenic spacers, as well as with 10 morphological characters. Our results suggest that at both sites  B. × wardii  is likely to be a hybrid between  B. alternifolia  and  B. crispa , and moreover, we confirm that most of the hybrids examined are F 1 s. That these plants are F 1 s is further supported by morphology, as no transgressive characters were detected.  B. crispa  was found to be the maternal parent in the Bahe (BH) population, from cpDNA evidence. However, in the Taji (TJ) population, the direction of hybridization was difficult to establish due to the shared cpDNA haplotypes between  B. alternifolia  and  B. crispa , however we still predicted a similar unidirectional hybridization pattern due to results from cross-specific pollination treatments which supported the “SI × SC rule”.    Conclusions  The presence of mainly F 1  hybrids can successfully impede gene flow and thus maintain species boundaries in parental species in a typical distribution of  Buddleja , i.e. in disturbed habitats.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-02909-7.

Natural hybridization between two butterfly bushes in Tibet: dominance of F1 hybrids promotes strong reproductive isolation