On 18 September 2003, Hurricane Isabel inundated northeastern North Carolina with heavy winds, rain, and storm surge that flushed high BOD organic materials and anoxic water from the floodplains adjacent to the lower Roanoke River and its tributaries into the river proper. Dissolved oxygen levels rapidly decreased and remained at or near 0 mg L-1 for 12 days causing an extensive fish kill throughout 25 km of the lower Roanoke River. Using boat-mounted electrofishing gear, we had surveyed fish assemblages at three fixed sampling sites on the lower Roanoke River during the summers of 2001 and 2002 and at two of the three sites one week prior to the hurricane in 2003. We returned one month after the hurricane to examine the fish assemblages at those two sites following the fish kill. We assessed recovery of the fish assemblages at the three lower Roanoke River sites by sampling during the summers of 2004 and 2005. One month after the hurricane and fish kill, species richness at the two lower Roanoke River sites had decreased by nearly 50%, and relative abundances of all remaining species were drastically reduced. The resulting fish assemblages were dominated by bowfin (Amia calva) and eastern silvery minnow (Hybognathus regius). Previously abundant sport fish such as largemouth bass (Micropterus salmoides) and bluegill (Lepomis macrochirus) were absent or represented by only a few individuals. Species richness and relative abundances of most species increased as the lower Roanoke River fish assemblages recovered a few years following Hurricane Isabel. Results from our study indicate that lower Roanoke River fish assemblages can recover from catastrophic disturbances, and that access to and from refugia is critical for successful recolonization of affected areas. We emphasize the need to identify areas of refugia and to elucidate fish movement patterns in response to large-scale disturbances.