Analyses of morphological and molecular data from recently collected specimens of Nemacheilus from Cambodia, Malaysia, and Thailand indicate that N. pallidus is a junior synonym of N. masyae, and an undescribed species of Nemacheilus occurs in large tributaries of the Mekong River in Thailand. The new species, described herein, is small—with a maximum-known standard length of 28.6 mm—and has a distinctive color pattern of dusky black bars along the side of the body that cross over the back and join the bars on the other side. Molecular phylogenetic analyses suggest that the new species is most closely related to N. masyae, which reaches a much larger size—to 66.2 mm SL—and otherwise is easily distinguished from the new species. The new species is known from the Songkhram and Mun river drainages in Thailand and appears to be restricted to the Khorat Plateau ecoregion of the Mekong River basin. Nemacheilus masyae occurs throughout mainland southeast Asia, including in the Chao Phraya, Mae Klong, Mekong, and coastal drainages of the Malay Peninsula.