The genus Mongolodiaptomus is widely distributed in stagnant water bodies in Southeast Asia. During a comprehensive collection of freshwater copepods from different areas in Thailand, a previously unknown species of calanoid copepod, Mongolodiaptomusphutakaensis sp. nov., was recorded. Representatives were found in a natural swamp located in the Kok Phutaka community forest in Khon Kaen Province, northeastern Thailand. The new species belongs to the "M.loeiensis species group" and most closely resembles M.loeiensis and M.mekongensis by having a distinct shape of the second exopodal segment of the male right P5, with enlarged proximal and distal parts of the outer margin as well as a bent and twisted principal lateral spine. The new species can be distinguished from its congeners by various characters in the males. The ventral surface of the right caudal ramus has two chitinous teeth and two knobs. The intercoxal plate is slightly produced distally and without any spine. The right P5 basis lacks a hyaline membrane on the inner margin but has a distinct spur-like chitinous process at the mid-distal margin on the posterior surface. The left P5 basis has a thin, longer hyaline lamella on the inner margin. The new species is rare, having been observed in only one out of approximately 5,000 surveyed locations in Thailand. A detailed morphological comparison and an up-to-date key to the Mongolodiaptomus species are presented. Their taxonomic characters, interspecies relationships, and biogeography are discussed.