Thinopyrum intermedium, which has many useful traits, is valuable for wheat breeding. A new wheat-Thinopyrum addition line, SN100109, was developed from the progeny of common wheat cultivar Yannong 15 and Th. intermedium. It was resistant to most races of Blumeria graminis f. sp tritici (Bgt), which caused powdery mildew in wheat, and its reactions were different from the reactions of gene Pm40 and Pm43. Genomic in situ hybridization (GISH) and molecular marker analysis were used to identify the genomic composition of SN100109. GISH results showed that SN100109 was a wheat-Th. intermedium disomic addition line containing one pair of J chromosomes, and the resistance gene was located on the alien additional chromosomes of SN100109. And four molecular markers BE425942, BF482714, Xgdm93 and BV679214 which were assigned to homologous group 2, were specific molecular markers of the additional chromosomes. All the results indicated that SN100109 contained one pair of 2J chromosomes. SN100109 can be used as a novel germplasm source for introducing powdery mildew resistance genes to wheat in breeding programs.