Within several plant species, a high variation in the composition of particular defence metabolites can be found, forming distinct chemotypes. Such chemotypes show different effects on specialist and generalist plant enemies, whereby studies examining interactions with pathogens are underrepresented. We aimed to determine factors mediating the interaction of two chemotypes of Bunias orientalis (Brassicaceae) with two plant pathogenic fungal species of different host range, Alternaria brassicae (narrow host range = specialist) and Botrytis cinerea (broad hostrange = generalist) using a combination of controlled bioassays. We found that the specialist, but not the generalist, was sensitive to differences between plant chemotypes in vivo and in vitro. The specialist fungus was more virulent (measured as leaf water loss) on one chemotype in vivo without differing in biomass produced during infection, while extracts from the same chemotype caused strong growth inhibition in that species in vitro. Furthermore, fractions of extracts from B. orientalis had divergent in vitro effects on the specialist versus the generalist, supporting presumed adaptations to certain compound classes. This study underlines the necessity to combine various experimental approaches to elucidate the complex interplay between plants and different pathogens. Plants produce a multitude of defensive compounds that mediate interactions with attacking organisms from different taxa 1. Generalists may be fended-off by (sets of) defence compounds effectively, while specialists instead use such compounds as host selection cues 2,3. These distinct roles of individual compounds in interactions with different natural enemies, including herbivores and pathogens, is discussed to be one of the major drivers of the evolution of diverse plant defences 4-6. A high variation in chemical defence profiles can be particularly found within plant species, in which so-called chemotypes are formed, that differ in the composition of a certain metabolite class 7-10. Several studies address the responses of insect herbivores to distinct chemical defence profiles in plant families or species 8,11,12. In contrast, only little is known about the role of phytochemical variation in interactions with pathogens (but see, e.g. 7). Various plant species of the Brassicaceae family show different chemotypes and are well-studied for interactions of certain chemotypes with plant enemies. For example, distinct chemotypes have been found in Arabidopsis thaliana 13,14 , Barbarea vulgaris 10,15 and Brassica oleracea 16,17. Interestingly, in B. vulgaris one chemotype is resistant to two herbivore species, while another is instead resistant to an oomycete pathogen 18 , underlining the importance to consider enemies from different taxa in chemo-ecological studies. Chemotypes in the Brassicaceae are typically characterised by variations in profiles of glucosinolates, a structurally highly diverse group of defence compounds 19. Glucosinolates are assumed to be largely involved in resistance of ...