The profitability of planting flood tolerant crops in flood plains relative to traditional row crops is evaluated under different assumptions concerning flood frequency and the level of government crop subsidy. The alternative crops evaluated are short rotation woody crops and herbaceous energy crops. The analysis is conducted for two growing environments: Louisa County, Iowa and Saline County. Missouri. The economic indicator used to value the alternative scenarios is annualized net return per acre. This indicator can account for the significant time lags between planting and harvesting of the two alternative crops. The results indicate that row crops dominate the flood tolerant crops until flood frequency approaches 50 percent. The positive environmental benefits that would occur from converting land to flood tolerant crops could justify additional government subsidies to offset, at least in part, the higher net returns of traditional crops.