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Lake Towuti is a tectonic-oligotrophic lake that located in Malili Complex, South Sulawesi. This lake is used for various purposes i.e. hydroelectric power plant, capture fishery, navigation, ecotourism and source of water for domestic uses. On the other side of this lake also supports a life of endemic species. It should be protected because the endemic species (carcinofauna: shrimps and crabs) and malacofauna (molluscs) already indicate a situation threatening the stock due to habitat quality changes and fishing activities. The aim of research is to know the habitat characteristics of carcinofauna and malacofauna in Lake Towuti as a basic for formulating the zoning criteria of endemic species in Lake Towuti. The study to be done in Lake Towuti from June to October 2009 at seven stations, namely: Tominanga, cape of Manu, Loeha Island, Hola-hola, Kawatang, Beau and cape of Bakara. Shrimp were collected using a scoop net with rope transect along 10 m distance and marked every 1 m. Crabs and molluscs was sampling using rope transect at a distance of 3, 6, 9 m (three plots) with a distance of 1 m transect the left and right. Shrimps and crabs samples preserved using 96 persen alcohol solution, whereas the molluscs samples using 4 persen formalin solution. Viewed ecological integrity (species and abundance of endemic species, water quality and substrate type) and ecological connectivity (covered of riparian vegetation and water macrophytes).The connection of the fish resources with environmental parameters were analyzed using principal components analysis. Habitat characteristics viewed from the environmental factors that are important for shrimp is high in pH and total nitrogen, total phosphorus, low turbidity and suspended material; substrate type is generally rock; high riparian vegetation cover of the group Borreria alata. For the crabs is low in turbidity, suspended solid and total phosphorus; high percentage of sand; high riparian vegetation cover of the group Bambusa, Borreria alata and Calophyllum sp. For molluscs is high in total nitrogen, total phosphorus and total organic matter; high percentage of sand, silt and clay; high riparian vegetation cover of the group Callophyllum sp. and Cyperus. Stations that have high species diversity for shrimp: Kawatang and Loeha Island, crabs: Hola-hola and cape of Bakara and molluscs: Tominanga and Hola-hola.