Abstract: The occurrence regularity of Metasequoia red blight disease in Shanghai and Nanjing were investigated and analysed. The pathogens of the disease were identified with morphological and molecular methods. Results showed: Metasequoia of single row or sporadic distribution was more sensitive than that with a higher canopy density. The resistance of Metasequoia that used as street tree was weak, and the disease was more serious than that planted in farm. The Metasequoia with a poor growth potential was more likely to be infected, especially the ones used as street trees. By isolation and culture of diseased tissue, artificial inoculation test, morphological observation and molecular identification by ITS analysis of the isolated strain, the pathogen of Metasequoia red blight was identified as Alternaria tenuissima and Pestalotiopsis heterocornis.