The small genus Macroclinidium, with five species, and the monospecific xMacropertya are endemic to Japan. Macroclinidium is characterized by unbranched stems with a few cauline leaves arranged near the middle part of the stem. xMacropertya, proposed as hybrid genus between Pertya ovata and Macroclinidium robustum, is characterized by having branched stems with many alternate leaves, and leafless basal portion. The cladistic relationships of Macroclinidium and xMacropertya based on 32 morphological characters were investigated. Catamixis, Ainsliaea and Pertya are the genera closest to Macroclinidium and xMacropertya. Oldenburgia from South Africa, is hypothesized to be sister to the latter five. Macroclinidium and xMacropertya are distinguished from Ainsliaea by their barbellate (vs. plumose) pappus, and from Pertya and Catamixis principally by their herbaceous (vs. shrubby) habit. The phylogenetic analysis resulted in four most parsimonious trees each with 80 steps. The analysis recovered Macroclinidium as monophyletic and xMacropertya as sister to Pertya. The inclusion of taxa of proposed hybrid origin (xMacropertya, Macroclinidium xkoribanum and M. xsuzukii) did not increase homoplasy conspicuously nor did it affect the outcome. A key to the species of Macroclinidium is provided, as well as morphological descriptions, illustrations, and a distribution map.