The family of Cryphonectriaceae (Diaporthales) includes many important tree pathogens, such as those that cause severe cankers on Eucalyptus trees. Recently, stem canker and cracked bark were observed on 8-year-old Eucalyptus grandis × E. urophylla trees in a plantation in southern China. Fruiting structures typical of Cryphonectriaceae fungi were observed on the surface of the diseased tissues. In this study, the isolated fungi were identified based on DNA sequence analyses and morphological characteristics, and their pathogenicity was tested on three Eucalyptus clones. DNA sequence comparisons of the internal transcribed spacer (ITS) regions (including the intervening 5.8S nrRNA gene), two regions of β-tubulin (BT2/BT1), and partial translation elongation factor1-α (TEF-1α), indicated that these isolates represent Celoporthe syzygii and one previously undescribed species. The undescribed species was also morphologically distinct from the other species of Celoporthe. The new species was described and named C. cerciana sp. nov. The results of this study based on the ITS, BT2/BT1, and TEF-1α sequences indicated that more than one haplotype was isolated from the same Eucalyptus tree. The findings of a previous study, whereby C. eucalypti was isolated from the same plantation as that of this study, revealed the high species diversity of Celoporthe within a single plantation, which is associated with a single Eucalyptus sp. in southern China. The results further suggested that hybridization may occur between C. syzygii and C. eucalypti. In addition to the Eucalyptus trees, C. syzygii was also isolated from native Melastoma candidum in the same Eucalyptus plantation. The inoculation results showed that these fungi isolated from E. grandis × E. urophylla and M. candidum are pathogenic to all three tested E. grandis hybrid clones. Significant differences in tolerance were observed between the tested Eucalyptus clones, suggesting that disease-tolerant Eucalyptus genotypes can be selected for disease management.