Background <p>Wide hybridization is crucial for broadening the genetic basis of common wheat. <i>Agropyron cristatum</i> (2<i>n</i> = 4<i>x</i> = 28, PPPP), a wild relative of wheat, harbors numerous favorable genes for genetic improvement. The variability related to the expression of alien genes in different wheat backgrounds is a crucial factor that limits the effective utilization of these genes.</p> Results <p>In this study, the introduction of chromosome 6P from <i>A. cristatum</i> into different wheat backgrounds resulted in different leaf colors: green in plants with the Fukuho background and yellow‒green in plants with the Jimai 22 background. Genetic analysis suggested that yellow‒green leaves were caused by gene interactions between chromosome 6P and genes from the Jimai 22 background, which negatively affected agronomic traits. To determine the locus on chromosome 6P responsible for yellow‒green leaves, six wheat–<i>A. cristatum</i> deletion lines and five wheat–<i>A. cristatum</i> translocation lines were crossed with Jimai 22 to produce F₁ progeny for leaf color investigation. We found that the F₁ progeny carrying the short arm of chromosome 6P (6PS) presented yellow–green leaves, and the relevant locus was ultimately mapped to 6PS (0.81-1.00). A total of 50 <i>A. cristatum</i> genes related to chlorophyll catabolite reductase and chloroplast development were annotated within this interval.</p> Conclusions <p>A locus on chromosome 6P of <i>A. cristatum</i> that caused a yellow–green leaf in the Jimai 22 background was mapped to chromosome 6PS (0.81-1.00). This study provides valuable germplasm for the study of leaf color and guidance for the use of valuable genes on <i>A. cristatum</i> chromosome 6P.</p>