Monilinia fructigena isolates from Japan were compared with isolates from Europe. General colony characteristics, stroma formation, growth rate and conidial dimensions were determined for six isolates each from both groups, as well as sporulation intensity on potato dextrose agar (PDA) and germ tube features. Potential differences in pathogenicity were tested on the pear cultivars ‘Conference’ and ‘Doyenné du Comice’, and on the apple cultivar ‘Cox's Orange Pippin’. A marked difference in stroma formation occurred, the area of stromatal plates ranged from 4·1 to 5·2 cm2 in the Japanese group, and from 0 to 0·9 cm2 in the European. The mean growth rate was significantly higher for Japanese isolates (t-test, P = 0·01). Length and width of conidia were significantly greater in European isolates (t-test, P = 0·01). Conidia measured on average 19×11·5 μm in European isolates, and 16×10 μm in Japanese ones when grown on cherry agar. On fruits, the difference in conidium size was even more pronounced. Sporulation intensity on PDA and germ tube features did not differ between both groups. No differences were found in latency period, lesion growth rate or sporulation intensity on apple and pear fruits between both groups. Together with previously published differences in the ITS region of ribosomal DNA, our results show that the Japanese isolates belong to a distinct species, Monilia polystroma sp. nov. A description of the anamorph is given, as well as a table summarising key features for all four brown rot associated Monilia species.