The availability of sequence data from large-scale EST (expressed sequence tag) projects has made it possible to develop markers directly from genes. In order to develop functional markers and the preparation of a transcript map (integrating of genes/transcripts to genetic map) of barley, more than 1000 ESTs/cDNAs including 589 RFLP (Restriction Fragment Length Polymorphism), 255 SNP (Single Nucleotide Polymorphism) and 185 SSR (Simple Sequence Repeat or microsatellite) markers have been developed. These markers provide a good resource for a variety of purposes including pedigree analysis, the study of marker-trait associations and comparative mapping in other cereals. A computational study suggests a theoretical transferability of barley markers to wheat (95.2%), rice (70.3%), maize (69.3%), sorghum (65.9%), rye (38.1%) and even to dicot species (~16%). Comparative mapping of 9 barley EST-SSRs in rye suggested the potential of barley markers to saturate the genetic maps of minor crop species having a shortage of molecular markers on their genetic maps. A comparison of 50 SSR and 50 SNP marker data for cladistic analysis on a set of six diverse barley genotypes showed that both marker types yield similar groupings. Therefore, gene-derived markers are a good resource for sampling the functional diversity in natural germplasm collection or breeding material.