Abstract – We investigated the variations of population of two cyprinids, Varicorhinus alticorpus and Varicorhinus barbatulus, using long-term survey data (1995–2004) in the subtropical island of Taiwan. Fish abundance data showed that at the mainstem stations, V. barbatulus which used to dominate in the higher altitude had declined significantly, while V. alticorpus that used to occupy only the lower altitude had spread upward. However, at the tributaries, trend of the populations of V. barbatulus were not significantly different over time, while populations of V. alticorpus were absent at higher altitude but began to increase at lower altitude. Environmental parameters revealed that sporadic high turbidity was observed at the mainstem stations, but not at the tributaries. Images taken before and after typhoon also showed habitat destruction by debris flow at the mainstem stations. As some models predicted that suitable fish habitats will shrink because of increasing water temperature due to global warming, we showed that fish distribution may be affected by habitat disturbance due to intensified storms sooner than the actual increase of water temperature.