Exploring the potential of novel sources of wheat material is immensely important to combat the ever-changing pathogen causing wheat rust disease, associated with huge losses worldwide. This study focused on assessing rust (YR) resistance in Chinese wheat hybrids, combining molecular markers and field testing over two years with estimation of the impact of selection. Out of 416 hybrids, 108 were selected based on disease scoring parameters, showing negative genetic advancement for rust severity and coefficient of infection. The maximum rust severity reached 100% for four hybrids during the year 2017–18 whereas 70% for three hybrids during the year 2018–19. The maximum coefficient of infection was observed for four hybrids which were 100% (2017–18), whereas 70% for three hybrids (2018–19). Molecular genotyping with a set of five yellow rust resistance genes linked markers revealed that the most frequent molecular markers was Yr18/Lr34 (among the YR markers), present in 92 out of 108 hybrids. All the five Yr genes were present only in 18 hybrids. Yr18 was the most common resistance gene detected in 85% hybrids, while Yr17 was the least detected gene (57%). Notably, the average coefficient of infection (ACI) was not directly associated with the number of resistant genes. Considering the overall performance, the hybrid lines 17BH002, 17BH057, 17BH073, 17BH109, 17BH123, 17BH128, 17BH190, 18BH026 and 17BH155 had an overall low yellow rust severity and co-efficient of infection and could be considering promising lines for further utilization. Clustering based on rust resistance genes categorized hybrids into five main clusters for YR resistance genes, showing variability among these valuable genetic resources. The observed variability in this study can be utilized for future breeding programs focused on developing resistant wheat varieties.