Sequences of nuclear ribosomal DNA ITS region were used to estimate phylogenetic relationships of Alnus. We recognize three major clades in Alnus, including subgenera Alnobetula, Clethropsis, and Alnus; subgenus Alnobetula is sister to subgenera Clethropsis and Alnus. The eastern Asian subgenus or section Cremastogyne is embedded in the subgenus Alnus clade. Alnus nepalensis is part of subgenus Alnus, not subgenus Clethropsis. Alnus maritima is part of subgenus Clethropsis (excl. A. nepalensis). Long and short branching pattern, sessile winter bud, and 2‐yr phenology are plesiomorphies in Alnus, while 1‐yr floral phenology and fall blooming are derived features. The simple axillary female inflorescence has evolved more than once in Alnus. Central and South American species of Alnus are derived from migrants from eastern Asia via the Bering land bridge and western North America. In subgenus Clethropsis, A. formosana of eastern Asia is more closely related to eastern North American species than to the other Asian species, A. nitida. The low sequence divergence within both the A. incana and A. viridis species complexes indicates their recent history of diversification in the circumpolar areas.