Fallopia japonica, originating from Japan, is a problematic invasive weed in both North America and Europe, especially in the UK. Our results indicate that a coevolved rust pathogen, Puccinia polygoni-amphibii var. tovariae has the potential to be a classical biological control agent for F. japonica. In this study, in order to find fungal endophytes that increase the pathogenic aggressiveness of P. polygoni-amphibii var. tovariae, we observed the development of rust disease in the field to determine uninfected and infected periods, and isolated them from the leaves of F. japonica in these periods. A total of 465 endophytic fungi were isolated from F. japonica in May and September of 2005 and 2006, which were uninfected and infected periods with the rust, respectively, and they were classified into 15 taxa. Two genera, Colletotrichum and Alternaria, were predominant as endophytes in F. japonica. Five genera were recovered from F. japonica only in September. Of these genera, one Phyllosticta isolate increased the virulence of P. polygoni-amphibii var. tovariae, following pre-inoculation with the endophyte ahead of the pathogen. Thus, it is suggested that the Phyllosticta would be a synergist of the rust disease, thereby increasing its potential as a biological control agent of F. japonica.