Abstract: Diaptomidae is one of the most common seen freshwater copepod fauna, the taxonomic study of this taxon is the basic information for the theoretical study of systemic zoology. Five species of genus Mongolodiaptomus (Copepoda, Calanoida, Diaptomidae) were reported in China before. This research reported a new species of Mongolodiaptomus from Hainan Island, which is the first record of Mongolodiaptomus mekongensis Sanoamuang & Watiroyram, 2018 in China. Through scanning electronic and light microscopy, the morphological characteristics are described and illustrated in detail. In addition, 18S rDNA gene sequences were also obtained for the first time to investigate phylogenetic position of this species. Morphological characteristics of female species are described in detail as follows: posterolateral wings of the fifth pedigerous segment were asymmetrical and right wing somewhat was larger than left. Left proximal part of genital somite broadly expanded and provided with laterally directed spine; Right proximal region of genital somite produced into posterolaterally directed, triangular process, tipped with variablespine, exceeded the middle of the genital somite. Morphological characteristics of male species are described in detail as follows: Right antennule transformed and geniculated, with 22 segments and the antepenultimate with comb-like process; Intercoxal plate of the right fifth leg produced into spine-like lobes on distal margin; The principal lateral spine on second exopodite of the right fifth leg is obviously bent; The right caudal ramus has two ventral chitinous prominences, one strong spiniform process on prominence proximally and one semi-circular ridges located at the end. The molecular phylogenetic analysis showed that M. mekongensis is closed related with the genus Eudiaptomus and Neodiaptomus. This study provides detailed morphological characteristics and molecular data for M. mekongensis, laying the foundation for future research on this species and genus Mongolodiaptomus.