Boltonia decurrens (Torrey and Gray) Wood (Asteraceae), a perennial species confined primarily to a 400-km stretch of the Illinois River floodplain, is threatened with extinction due to the destruction of its natural habitat. Construction of a system of levees along the Illinois River has altered flood patterns during the last 100 years, converting wet prairies and natural marshes into cropland. Remaining shore habitats have been modified by altered flooding regimes. The flood of 1993 exceeded 100-year records on the Mississippi River, but was much less severe on the Illinois River. A gradient of flood severity on the Illinois River, from the area of confluence with the Mississippi River to a site 267.5 km upriver, provided an opportunity to study the effects of flooding on the vegetation at three B. decurrens sites which experienced different flood regimes. A comparison of pre-and post-flood data (1991 and 1994) revealed that the flood altered site vegetation. Species richness declined in all three study areas by an average of 34% and species diversity declined at two sites (11% and 37%). Populations of B. decurrens increased in size at all three locations (5-, 10-and 400-fold) following the flood, with the greatest increase occurring at the two sites which had the most severe flooding. The results suggest that the removal of competing species by flood waters may be an important factor in maintaining populations of B. decurrens in the floodplain.