To address the evolution and geographical diversification of the genus Zelkova (Ulmaceae) a phylogenetic analysis of morphological data and the sequences of the internal transcribed spacers (ITS1 and ITS2) of nuclear ribosomal DNA were used. Cladistic analyses suggested that the Chinese species Z. schneideriana and Z. sinica are basal within Zelkova. The western Asian Z. carpinifolia either appears nested between the East Asian Z. schneideriana and Z. sinica and a clade formed by the Japanese Z. serrata and two Mediterranean species, Z. abelicea and Z. sicula (ITS), or forms a clade with Z. serrata that is sister to a clade Z. abelicea plus Z. sicula (morphology). Nucleotide data suggested that gene flow occurred between Z. schneideriana and Z. serrata, and Z. carpinifolia and a lineage ancestral to Z. abelicea/sicula. Character evolution in Zelkova appears to have gone from long leaves with numerous secondary veins, coarse to shallow teeth with blunt or slightly pointed apex and small stomata, to leaves that are either long or short with numerous or few secondary veins, coarse teeth with cuspidate or obtuse apex or conspicuously shallow teeth, and dimorphic stomata displaying ‘giant stomata’ surrounded by a ring of small stomata or uniform large stomata. These results are in agreement with fossil data. Early Cainozoic fossils attributed to Zelkova from North America and Central Asia closely resemble the modern Z. schneideriana and Z. carpinifolia. The genus could have originated in the northern Pacific area and migrated to Europe after the Turgai Strait was closed during the Late Oligocene. Geographical differentiation may have started with the isolation of Chinese populations (leading to modern Z. schneideriana and Z. sinica) from high-latitude Eurasian (North American) populations. This widespread Early Cainozoic type may have diversified into the western Asian Z. carpinifolia and the more derived Japanese and Mediterranean species during the latest Cainozoic. The modern Japanese and European/western Asian species would have differentiated relatively late, while two locally endemic Mediterranean species are the result of the cooling and development of a Mediterranean climate belt in Europe during the Pleistocene. Fossils from the Miocene and Pliocene of Europe resemble modern Z. carpinifolia and Z. serrata. Differentiation of the two Mediterranean species Z. abelicea and Z. sicula in the Late Cainozoic cannot be traced by leaf morphology.