The relationships among species of the genus Chroogomphus were inferred from morphology and the nucleotide sequences of the internal transcribed spacer (ITS) regions of the nuclear ribosomal gene Cluster. Our analysis revealed that: (1) the monophyly of Chroogomphus was well supported but a previous two-section infrageneric division of Chroogomphus is not valid. (2) Geographical divergences of Chroogomphus in the Northern Hemisphere were evident. Most species had relatively narrow distribution ranges, and taxa with intercontinental distributions were uncommon. In Far East Asia and central Europe, C. rutilus had a sympatric distribution pattern as C. purpurascens but with plant hosts in different subgenera of Pinus. Between East Asia and North America vicariously paired or closely related species of Chroogomphus were present. (3) During the co-evolution of Chroogomphus with its mycorrhizal hosts, host specificity generally increased yet host-switches between the two subgenera of Pinus took place. (4) Seven species were collected from China, four of which were described as new and illustrated with line drawings. In addition, a new combination, C. albipes, was proposed, and a key to the Chroogomphus species from China was provided.