Eighty one Setosphaeria turcica isolates were collected from 13 corn planting areas of Yunnan Province during 2007 to 2009, which were identified by using two sets of the corn differentials containing single Ht resistance genes and their mating types were analyzed by using molecular markers. The results showed that both physiological races and mating types of the pathogen were very complicated in Yunnan Province. The isolates could be divided into 11 races including 0, 1, 2, 3, 12, 23, 2N, 3N, 12N, 23N and 123N, among which 123N could overcome all of the single dominant resistance genes of the differentials to S.turcica and accounted for 22.2%. Based on the molecular markers, the 81 isolates were divided into three mating types including A, a and Aa, and neuter, accounting for 49.4%, 12.3%, 29.6% and 8.6%, respectively. In addition, different races and mating types of S.turcica existed in the same area.