Abstract: To know the pathotype and population structure of Cochliobolus heterostrophus in Fujian Province, 247 C. heterostrophus isolates, collected from seven regions in Fujian Province during 2014-2015, were used to study the lesion types of leaves of‘C103T’,‘C103C’,‘C103S’and‘C103’with different cytoplasm, using the method of measuring lesion length. The results showed that all the tested isolates could cause disease incidence in four corn varieties, with the average value of lesion length as 1.15-5.40 mm, 1.06-4.70 mm, 1.09- 4.84 mm and 1.15-5.21 mm, respectively. According to their length, the lesions were divided into I and II type, and the frequency of the tested isolates in the two lesion types was 80.26% and 19.74%, respectively. Base on the lesion type of each isolate on the four corn varieties in order, the tested isolates were divided into 15 pathotypes, the pathotype of CHP15 (lesion type of“I-I-I-I”) and CHP11 (lesion type of“II-I-I-I”) was dominant type and sub-dominant type, respectively. The percentage of dominant and sub-dominant type was 57.49% and 9.72%, respectively. The composition of pathotypes and frequencies of the tested isolates from different locations exhibited abundant diversity. In addition, among the 235 isolates from O races, 14 pathotypes were observed. There was significant pathogenicity differentiation among these isolates.