A new species of gudgeon, Microphysogobio xianyouensis, is described from Mulan River in Fujian Province, southeastern China. M. xianyouensis appears to be closely related to M. brevirostris (Günther, 1868) of Taiwan. However, it can be well distinguished based on a combination of meristics, morphometric measurements, color pattern and molecular data. A molecular phylogenetic analysis of species of Microphysogobio from southeastern China and Taiwan based on concatenated mitochondrial Cyt b and D-loop genes is presented and tree topology strongly supports that M. xianyouensis as a distinct species and sister to M. brevirostris. Our molecular evidence agreed with Bănărescu's proposed taxonomic viewpoint, the tree topology reveals that the type species of the genus Huigobio, H. chenhsienensis, is nested within several valid species of Microphysogobio, and Huigobio is confirmed to be a junior synonym of the genus Microphysogobio.