In total, 455 Monilinia isolates from stone fruits collected from several provinces (cities) in China from 2003 to 2009 were identified to species based on morphological characteristics, molecular identification, and the sequence of the internal transcribed spacer (ITS) regions 1 and 2 and the 5.8S gene of the ribosomal RNA. Overall, four species were detected (Monilinia fructicola, M. fructigena, M. laxa, and Monilia polystroma). M. fructicola was the most prevalent (93.0%) followed by M. fructigena (4.8%), M. laxa (2.0%), and Monilia polystroma (0.2%). M. fructicola and M. fructigena were found on peach, plum, and apricot; M. laxa was found only on apricot, cherry (in an organic orchard), and wild peach; and Monilia polystroma was found only on plum in Heilongjiang. The pathogenicity of Monilinia fructicola, M. laxa, and M. fructigena did not significantly differ on wounded nectarine and apricot, indicating that the differences in frequency of occurrence were not linked to virulence. Phylogenetic analysis based on ITS sequences showed that the isolates of M. laxa and M. fructigena from China differed from isolates of these species from other countries, and that the difference led to the separation of the isolates from China and those from other countries into different phylogenetic groups. Further study is needed to determine whether they are cryptic species.