Naked caryopsis trait in barley is controlled by a single recessive gene, nud, located on chromosome 1 (7H); it prevents adhesion of the lemma and palea to the caryopsis (hulless barley). To identify new markers closely linked to nud, to facilitate marker-assisted selection of the naked trait, we applied the RAPD protocol coupled with the Bulked Segregant Analysis strategy on the barley Proctor (hulled) x Nudinka (naked) mapping population. We identified two RAPD markers and only the most tightly linked, was successfully converted into a more specific SCAR marker. This together with other 6 markers were mapped onto a reference map. A naked/hulled barley germplasm was collected to individuate the haplotype structure surrounding the nud locus, employing most tightly linked markers. The response to leaf stripe disease was evaluated among a subset of the same germplasm, in order to investigate any possible associations between disease incidence and other recorded traits.