Background <p>Rice is the primary source of calories for a large portion of the global population. Most rice hulls are of the trichome-type and produce dust, which can cause respiratory allergies and environmental concerns during handling. By contrast, glabrous-type hulls reduce storage volume and minimise dust, making processing cleaner and more eco-friendly. Despite the advantages of glabrous rice as a breeding resource, no molecular markers are available for the effective selection of this trait.</p> Results <p> <?tk 2?>In this study, we developed a novel cleaved amplified polymorphic sequence (CAPS) marker specifically designed to select glabrous hulls in rice. Using the sequence information of the Kompetitive Allele-Specific Polymerase Chain Reaction (KASP) marker KJ05_001, closely linked to <i>GLR1</i>, we identified an <i>Mse</i>I recognition site for targeted digestion. This sequence was used to create the <i>GLR1</i>_CAPS marker, showing tight linkage to <i>GLR1</i>. The effectiveness of this marker was tested in 290 diverse rice germplasm lines, confirming its broad applicability.</p> Conclusions <p> <?tk 2?>Overall, the <i>GLR1</i>_CAPS marker is an efficient and reliable tool for breeding programs focused on the development of glabrous rice varieties. By facilitating accurate selection of this trait, the developed marker offers substantial improvements in rice storage, handling, and processing, contributing to more sustainable and allergy-friendly agricultural practices. This novel molecular marker represents an important advancement in rice breeding and opens new avenues for the development of rice varieties with reduced environmental and health impacts.</p> Graphical Abstract <p></p>