All diploid species of Hordeum have been included in phylogenetic analyses of four molecular data sets supposedly from three different linkage groups. Two data sets stem from the nuclear genome: partial DMC1 (disrupted meiotic cDNA1) sequences (chromosome 3 in H. vulgare) and partial EF-G (elongation factor G) sequences (chromosome 2 in H. vulgare). The other two data sets are RFLP data and sequence data, rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase), from the plastid genome. Incongruence length difference tests show that the two nuclear and the two plastid data sets, respectively, are congruent, whereas the nuclear data and the plastid data are incongruent. The greatest incongruence is caused by the two Eurasian subspecies of H. marinum. The nuclear data support monophyly of the species, but the plastid data group one of the subspecies among the American taxa. The explanation is most likely lineage sorting. Based on a combined analysis of all data sets a new infrageneric classification of Hordeum including only monophyletic groups is presented. One new taxon, Hordeum L. sect. Sibirica (Nevski) G. Petersen & Seberg, stat. nov., is proposed. The distribution of selected morphological characters is discussed.