Tor douronensis (God Fish) species are endemic freshwater fish that only live in Kuningan District. Originally these fish scattered in the pool Cigugur, Cibulan, Balong Kambang, Darma Loka and Balong Dalem. However, since 2006 the god fish that existed in Balong Dalem extinct. This study aims to analyze the possible factors causing extinction of the god fish in situ Balong Dalem. The study was conducted during May 2017. The results showed that there were 11 phytoplankton and 13 genera of Gomphonema, Stigeoclonium, Desmidium, Closterium, Navicula, Spirulina, Phormidium, Melosira, Gloeotrichia, Oedogonium, Hyalodiscus, Moscocrocis and Cladophora. While zooplankton found 3 genus of Cyclops, Rotifera and Tanypus. The results showed that the abundance, diversity and uniformity of zooplankton correlated positively with pH, temperature, DO and water flow but not with others. Condition of water quality (physical-chemical parameter) Balong Dalem in bad condition, low productivity and labile. Condition of substrate base there Balong Dalem in the form of sand and fine mud. All of these conditions caused the extinction of Tor douronensis in situ Balong Dalem.