Several large, uncharacteristic wildfires occurred on the Boise National Forest in Southwest Idaho, from 1986 to 2003. From 1987 to 1994, severe wildfires burned almost 50% of the ponderosa pine forest types (about 200,000 ha). The intensity of the fires varied across the landscape, with a mix of low to moderate severity, and lesser amounts of high burn severity. After the fires, localized debris flows favored smaller order streams in watersheds less than 4000 ha in size, where there had been mostly high severity burning. Locally, areas experiencing high heat and post-fire debris flows had reduced fish numbers and altered fish habitats. Uncharacteristic wildfires on the managed portions of the Boise National Forest appeared to have more pronounced, short-term effects on fish habitats as compared with characteristic wildfires in the Central Idaho Wilderness. Even in the most severely impacted streams, habitat conditions and trout populations improved dramatically within 5–10 years. Post-fire floods apparently rejuvenated stream habitats by exporting fine sediments and by importing large amounts of gravel, cobble, woody debris, and nutrients, resulting in higher fish productivities than before the fire. These observations suggest that important elements of biodiversity and fish productivity may be influenced, or even created by fire-related disturbances. In some cases, habitats that were completely devoid of salmonid fishes just after the debris floods, were later re-colonized with migrants returning from downstream or nearby tributary rearing habitats. Re-population was likely enhanced by higher fecundity, homing instinct, and greater mobility of the larger migratory fish. Ecosystem restoration activities that reduce both short- and long-term threats of uncharacteristic wildfire on imperiled fishes could be emphasized in areas where local populations may be weak and/or isolated, but potentially recoverable. But forest ecosystem restoration alone may not reduce risks to fish if existing habitat conditions and isolation are limiting the population.