ABSTRACT: BACKGROUND: Many studies have been done to find out the molecular mechanism of systemic acquired resistance (SAR) in plants in the past several decades. Numbers of researches have been carried out in the model plants such as arabidopsis, tobacco, rice and so on, however, with little work done in woody plants especially in fruit trees such as apple. Components of the pathway of SAR seem to be extremely conserved in the variety of species. Malus hupehensis, which is origin in China, is strong resistance with rootstock. In the study, we attempted to make the expression pattern of pathogenesis related (PR) genes which were downstream components of the SAR pathway in response to salicylic acid(SA), methyl jasmonate(MeJA) and 1-aminocyclopropane-1-carboxylic acid(ACC) in Malus hupehensis. FINDINGS: In order to analyze the expression pattern, the partial sequence of three PR genes from Malus hupehensis, MhPR1, MhPR5 and MhPR8 was isolated. These three PR genes were induced by SA, MeJA and ACC. However, MhPR1, MhPR5 and MhPR8 performed a distinct pattern of expression in different plant organs. MhPR5 and MhPR8 were basal expression in leaves, stems and roots, and MhPR1 was basal expression only in stems. The expression of MhPR1, MhPR5 and MhPR8 was enhanced during the first 48 h post-induced with SA, MeJA and ACC. CONCLUSIONS: The results showed that a distinct pattern of expression of PR genes in Malus hupehensis which differed from the previous reports on model plants arabidopsis, tobacco and rice. MhPR1, MhPR5 and MhPR8 were induced by SA, MeJA and ACC, which were regarded as the marker genes in the SAR response in Malus hupehensis. In contrast with herbal plants, there could be specific signal pathway in response to SA, JA and ET for woody plants.