In cereals, granule-bound starch synthase I (GBSSI)-deficient mutants accumulate glutinous (amylose-free) starch in their storage tissues. The amylose-free starch produced by waxy ( wx ) mutants of hexaploid bread wheat ( Triticum aestivum L.) is used in cakes and breads. However, wx mutants of diploid wheat ( T. monococcum L.) have so far no commercial applications. In this study, we identified a mutation in exon 6 of GBSSI in a diploid wheat wx mutant that resulted in the replacement of Trp355 with a stop codon. Molecular markers were developed for the rapid screening of the mutation, which should allow the selection of heterozygous and homozygous plants during backcrossing. This will facilitate the improvement of the agricultural traits of the wx mutant and the generation of new amylose-free wx lines.