Stripe rust and powdery mildew, caused respectively by Puccinia striiformis f. sp. tritici (Pst) and Blumeria graminis f. sp. tritici (Bgt), are globally important diseases of wheat. Genes transferred to wheat from wild species are often associated with deleterious traits. In this study, a wheat-Thinopyrum intermedium germplasm line CH7124 was characterized by a combination of resistance evaluation, cytological observation and genomic in situ hybridization (GISH). Disease screening demonstrated this line was highly resistant to both Pst races CYR29, CYR31, CYR32 and CYR33 and Bgt isolates E09, E20, E21 and E26, which are the most widely virulent pathotypes in China and virulent to most of the known resistance genes, and the resistance derived from Th. intermedium. Genetic analysis of the F1, F2, F3 and BC1 populations from resistant line CH7124 revealed that the resistance to powdery mildew and stripe rust was controlled by a single dominant allele. Mitotic observation showed that CH7124 had 42 chromosomes, and the chromosomes in most pollen mother cells of its F1s involved wheat genotypes Chinese Spring and Mianyang 11 at PMC MI formed 21 bivalents, averaging, respectively, 20.73 in 102 cells and 20.74 in 87 cells, suggesting stability of CH7124 in cytology and regular pairing with common wheat. As no signal could be detected when using genomic Th. intermedium DNA as a probe in the GISH experiment, the introgressed alien chromatin in this line was very small and cytologically undetectable, further indicating that CH7124 is a cryptic wheat-alien introgression line. This study showed that CH7124 appears to serve as a novel resistance source for wheat breeding.