Apple ring rot and Botryosphaeria canker are severe diseases affecting apple production in China, but there is confusion regarding which pathogens cause these diseases and their similarity to other diseases, such as white rot of apple, and ring rot and Botryosphaeria canker of pear. In this study, the pathogen of apple ring rot in China was compared with the pathogen of apple ring rot in Japan and Korea, the pathogen of Botryosphaeria canker of apple and pear in China, the pathogen of pear ring rot in China, and the pathogen of white rot of apple in the United States. Comparisons were based on morphology, pathogenicity on branches and fruit, and sequences of rDNA in the internal transcribed spacer region and of the β-tubulin and actin genes. Results showed that the causal agent of apple ring rot and Botryosphaeria canker of apple in China was Botryosphaeria dothidea, which has also been reported to be the pathogen of apple ring rot in Korea and Japan. Pathogenicity tests showed that B. dothidea infection on apple and pear branches may induce wart or canker symptoms depending on the conditions. These results are consistent with the hypothesis that the same pathogen causes the wart symptom of apple ring rot and the Botryosphaeria canker symptom on apple branches in China. The results also suggest that apple ring rot and white rot are the same disease and are caused by B. dothidea. Finally, B. dothidea isolates from pear and other fruit or forest trees may serve as inoculum for apple ring rot.