Abstract:[Background] Powdery mildew (PM) is one of the most devasting diseases in rose and other ornamental plants, however, there is no better way to control it untill now. Previous studies have demonstrated that endophytes are beneficial to host plant’s disease resistance. Rosa multiflora and R. multiflora var. carnea is a PM resistant and susceptible rose species, respectively. It’s not clear about the difference of their fungal endophytic communities and their function. [Objective] To study the difference of the fungal endophytic communities between two rose species and to understand the possible role of endophytes on PM resistance. [Methods] The culturable endophytic fungi (EF) were isolated from two rose species at different developing stage of PM by traditional EF isolation methods. [Results] A total of 2?003 endophytic fungi were isolated from 2 880 tissue segments of 24 samples of two rose species, of which 1 333 from R. multiflora and 670 from R. multiflora var. carnea. The isolates were identified to 30?taxa according to the morphological charateristics and the rDNA internal transcribed spacer (ITS) analysis, of which Alternaria alternata, C. truncatum and Phomopsis amygdali were the dominant genera of two rose species at different developing stage of PM. Contrary to this, Seimatosporium sp., Coprinellus sp. and Chaetomium globosum etc. were only found in R. multiflora or R. multiflora var. carnea. [Conclusion] The fungal endophytic community of R. multiflora showed significantly difference from that of R. multiflora var. carnea. The average colonization rate (CR) of EF from R. multiflora was significantly higher than that of R. multiflora var. carnea at each developing stage of PW (P<0.05, Chi-square test). The role of the specific and dominant EF of R. multiflora in PM resistance were further studied in the future.