We examined the daytime habitat use of highly endangered bagrid catfish Pseudobagrus ichikawai before and after rare catastrophic floods in the tributary flowing in the Miya River basin of Mie prefecture, Japan. The bagrid catfish were consistently more abundant in the pool and sheltered interstitial spaces formed by cobble and boulder substrates. Despite that the tremendous (>15-fold increase in water level) floods did not have recognizable effects on catfish at the reach or channel-unit scales, shifts in spatial distribution of individuals occurred at a microhabitat scale over the floods. Only 20% of the patches (permanent habitat) with resident fish before the floods contained individuals after the events whereas individuals appeared or disappeared in other patches (temporary habitat) after the events. In one permanent habitat, individuals of various sizes persistently occupied spaces beneath single boulder, and number of individuals increased by more than 3-fold over the events. The physical environment of permanent habitat was characterized by greater areas covered by angular (not spherical) boulders and deep water depth. These results suggest that it is crucially important to preserve hydraulic refuge habitats with angular boulders in deep pools in order to maintain suitable habitat environments and viable populations of bagrid catfish.