Flowers which show cleistogamy (CL) remain closed during pollen shedding, and thus are predominantly self-pollinated. CL in barley is controlled either by the single, multi-allelic gene cly1 located on the long arm of chromosome 2H, or by two closely linked, epistatic genes (cly1 and Cly2). Here, we have taken advantage of the co-linearity which exists between chromosome 2H of barley and rice chromosome 4 to generate de novo markers targeted to the CL region, and these have been used to construct a localized high resolution genetic map. While synteny is largely conserved in this region, the critical 18 cM barley segment appears to be inverted with respect to the equivalent 1.6 Mb physical stretch of the rice genome. The cly1 locus was located in a 0.76 cM region of barley genetic map, and rice orthologue of cly1 (if there is one) is one of the 11 genes predicted to lie within 90 kb interval of rice genome.