Biosynthesis of phytoalexins is a plant defence strategy against pathogens. Shoots of the apple (Malus × domestica) cultivar ‘Holsteiner Cox’ formed biphenyls and dibenzofurans when inoculated with the fire blight bacterium, Erwinia amylovora. The phytoalexins were only present in the transition zone of stems, whereas the leaves were devoid of the defence compounds. The scaffold of the phytoalexins is formed by biphenyl synthase (BIS), a type III polyketide synthase. In apple, BIS is encoded by a gene family, members of which fall into four subfamilies. Representative BIS cDNAs were cloned from fire blight-infected shoots of ‘Holsteiner Cox’ and functionally expressed. The preferred starter substrates were benzoyl-CoA and salicoyl-CoA, leading to the formation of 3,5-dihydroxybiphenyl and 4-hydroxycoumarin, respectively, in the presence of malonyl-CoA as extender molecule. The four subfamilies were differentially regulated after inoculation of shoots with E. amylovora. The BIS3 gene was expressed in stems, with maximum transcript levels in the transition zone. The BIS3 protein was immunochemically localized to the parenchyma of the bark. Dot-shaped immunofluorescence was restricted to the junctions between neighbouring cortical parenchyma cells. Leaves contained transcripts for BIS2 which, however, were not translated into immunodetectable BIS protein. The understanding of phytoalexin metabolism may aid in improving apple resistance to fire blight.