Abstract Background Nonhost resistance is the outcome of most plant/pathogen interactions, but it has rarely been described in Rosaceous fruit species. Apple ( Malus x domestica Borkh.) is a nonhost for Venturia pyrina , the scab species attacking European pear ( Pyrus communis L.). Reciprocally, P. communis is a nonhost for Venturia inaequalis , the scab species attacking apple. The major objective of our study was to compare the scab nonhost resistance in apple and in European pear, at the phenotypic and transcriptomic levels. Results Macro- and microscopic observations after reciprocal scab inoculations indicated that, after a similar germination step, nonhost apple/ V. pyrina interaction remained nearly symptomless, whereas hypersensitive reactions were observed during nonhost pear/ V. inaequalis interaction. Comparative transcriptomic analyses of apple and pear nonhost interactions with V. pyrina and V. inaequalis , respectively, revealed considerable differences. Very few differentially expressed genes were detected during apple/ V. pyrina interaction, which is consistent with a symptomless type I nonhost resistance. On the contrary, numerous genes were differentially expressed during pear/ V. inaequalis interaction, as expected in a type II nonhost resistance involving visible hypersensitive reaction. Pre-invasive defense, such as stomatal closure, was detected, as well as several post-invasive defense mechanisms (apoplastic reactive oxygen species accumulation, phytoalexin production and alterations of the epidermis composition). In addition, a comparative analysis between pear scab host and nonhost interactions indicated that, although specificities were observed, two major defense lines were shared in these resistances: cell wall and cuticle modifications and phenylpropanoid pathway induction. Conclusion This first deciphering of the molecular mechanisms underlying a nonhost scab resistance in pear offers new possibilities for the genetic engineering of sustainable scab resistance in this species.