Abstract: The Black stem rot was found in Song county and stem wilt was found in Luoning county in Henan Province. In order to identify the pathogenic species of the two diseases, two fungal strains were isolated from diseased stems with typical symptom through the methods of tissue separation. The strains were identified by morphological identification method and pathogenicity test according to Koch's postulation. Its rDNA ITS sequence was analyzed for similarity. The results showed that colony of strain I was radial pattern, and turn to petaloid gradually, antheridium was mitriform or irregular on OA, identified as Pythium vexans, which infected tobacco cased stem black rot was first reported in Henan province. The colony of strain Ⅱ was initially white, the mid of colony gradually turn lividity, conidium was septate or aseptate, ascus was clavate, ascospore was fusiform, septate, constriction on diaphragm, sexual stage was Didymella ligulicola, Asexual period was Ascochyta chrysanthemi, invasion tobacco was the first report.