The invention provides a molecular marker for rapidly detecting scab-resistant gene of elytrigia elongata. The molecular marker takes two wheat-elytrigia elongata aline substitution lines 7el1 and 7el2 as parents to construct an F2 segregation population, screens out a single plant recombining bear a target site and multiplies the single plant into a strain, searches a molecular marker closely linked with the strain through a head scab phenotype identification technology, is used for the early marker gene aided selection of wheat scab-resistant breeding and scab-resistant character, and can improve the breeding efficiency.