The systematics of the gecarcinucid genus Balssiathelphusa Bott, 1969 is revised. Balssiathelphusa has an atypical distribution pattern for a freshwater crab genus, with the four known species recorded from Sumatra, Borneo and Natuna Islands in the South China Sea. The type species, Para-Peri-thelphusa sucki Balss, 1937 [sic, see infra], is redescribed and figured, and the genus is redefined to include B. sucki, B. cursor Ng, 1986, from East Kalimantan in Indonesian Borneo, and a new species, B. inopinata n. sp., also from East Kalimantan. The type locality of B. sucki was reported as southeastern Sumatra, but the available evidence suggests the holotype was actually collected from South Kalimantan in Borneo. Balssiathelphusa natunaensis Bott, 1970, from Natuna Island, is transferred to a new monotypic genus, Natunusa n. gen., while B. phasma Ng & Guinot, 2014, collected from a cave in East Kalimantan, is referred to a separate genus, Lemurophusa n. gen. A new species, L. empusa n. gen., n. sp., is also described from another karst system in East Kalimantan, whereas a juvenile female from a nearby cave in East Kalimantan is treated as Lemurophusa sp. Particular attention was paid to the thoracic sternum and its sutures, to the median bridges between the sternites, as well to the median line, characters often overlooked but that are particularly useful in this group of small gecarcinucid crabs.