Members of the genus Echiniscus C.A.S. Schultze, 1840 are mostly unisexual, with thelytokously reproducing females. Therefore, every newly described dioecious species in the genus is particularly interesting. Here, we describe Echiniscus masculinus sp. nov. from Gunung Kinabalu, the highest peak of Borneo and the entire Southeast Asia. The new species belongs in the predominantly parthenogenetic E. virginicus complex, and its females are confusingly similar to females of the pantropical E. lineatus Pilato et al., 2008, another member of this group. However, genetic evidence and noticeable sexual dimorphism clearly delineate the new species. Males of E. masculinus sp. nov. are unlike females in the body proportions, cuticular sculpturing, and appendage configuration. The new discoveries provide a justification to review the current knowledge about evolution and forms of sexual dimorphism within Echiniscus.