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Microdous amblyrhynchos, a new species, the second one in the genus, from the family Odontobutidae, is described from the Hongshui River, in the upper reaches of the Xijiang River of the Pearl River drainage, Baise City, Guangxi Zhuang Autonomous Region, southern China. This species is distinguished from its only congener, M. chalmersi, by the blunt snout (vs. pointed); mean snout length/head length ratio 0.27 (vs. 0.3); eye not extending outward (vs. protruding); mean interorbital width/head length ratio 0.25 (vs. 0.11). Additionally, the results of molecular phylogenetic analysis confirmed that M. amblyrhynchos sp. nov. is distinct from its sister species, M. chalmersi.