The short awn 2 (lks2) and dense spike 1 (dsp1) genes are unique to East Asian barley. These two spike-related morphological genes are important because they may be involved in stable production and local adaptation. As a first step of their positional cloning, molecular mapping was conducted in 98 F₂ plants derived from a cross between Karafuto Zairai and Aizu Hadaka 3. The dsp1 gene was mapped to the proximal region of the short arm of chromosome 7H. The lks2 gene was located on the long arm of 7H and flanked by EST-based markers k04151 and k06123, with distances of 0.5 cM in the proximal side and 1.0 cM in the distal side. Both k04151 and k06123 shared homology to rice genes on chromosome 6 that were separated with the physical distance of 5.6 Mbp. In this interval, rice–barley microsynteny was exploited for marker enrichment. Of 57 rice genes attempted, 15 (26.3%) yielded polymorphic EST-based markers. Breakdown of collinearity was found in the candidate region of lks2, suggesting occurrence of structural changes in the chromosome region harboring lks2 during divergence of barley and rice from a common ancestor.