Gene transfer from transgenic crops to their weedy relatives may introduce undesired ecological consequences that can increase the fitness and invasiveness of weedy populations. Here, we examined the rate of gene flow from abiotic stress-tolerant transgenic rice that over-express AtCYP78A7, a gene encoding cytochrome P450 protein, to six weedy rice accessions and compared the phenotypic performance and drought tolerance of their hybrids over generations. The rate of transgene flow from AtCYP78A7-overexpressing transgenic to weedy rice varied between 0% and 0.0396%. F1 hybrids containing AtCYP78A7 were significantly taller and heavier, but the percentage of ripened grains, grain numbers and weight per plant were significantly lower than their transgenic and weedy parents. The homozygous and hemizygous F2 progeny showed higher tolerance to drought stress than the nullizygous F2 progeny, as indicated by leaf rolling scores. Shoot growth of nullizygous F3 progeny was significantly greater than weedy rice under water-deficient conditions in a rainout shelter, however, that of homozygous F3 progeny was similar to weedy rice, indicating the cost of continuous expression of transgene. Our findings imply that gene flow from AtCYP78A7-overexpressing transgenic to weedy rice might increase drought tolerance as shown in the pot experiment, however, increased fitness under stressed conditions in the field were not observed for hybrid progeny containing transgenes.