The Malay Archipelago comprises thousands of islands that house a variety of biomes, from tropical rainforests of Borneo, Sumatra and Celebes to the Lesser Sundas deciduous forests. In this paper, we present an extensive genetic and morphological dataset for the genus Kristenseniscus, demonstrating the presence of the walteri complex that contains several pseudocryptic species. One of them, Kristenseniscus exanthema sp. nov., is described from Ambon and Seram (the Moluccas). First genetic data are released for two potentially pantropical Echiniscus species: E. africanus Murray, 1907 and E. pusae Marcus, 1928. Furthermore, Echiniscus minutus sp. nov. (Sulawesi Tengah), exhibiting trunk spines and contrasting dorsal sculpturing that comprise both pores and epicuticular granules, is found to constitute a separate evolutionary lineage within the Echiniscus spinulosus morphogroup (epicuticular granules are typically absent in the spinulosus group). Based on the phylogenetic reconstructions involving ca. 80 spp. of echiniscids representing the Echiniscus evolutionary line, we hypothesise that the tropical and subtropical regions served as the main radiation zone for this heterotardigrade clade. Finally, Pseudechiniscus (Meridioniscus) celebesiensis sp. nov. (Sulawesi Tengah) is a characteristic species with an apomorphic lack of claw spurs and intricate dorsal cuticular sculpturing. Our findings suggest that the tropical areas of the globe harbour a phylogenetically important but yet mostly uncovered portion of Earth’s tardigrade diversity.