In order to assess the ecological fitness of anti-fungal transgenic rice lines, E121-2-1 and E122-2-9, their fitness component-related traits such as agronomic traits, reproductive capability, pollen viability, seed viability, seed bank persistence and volunteer possibility were analysed by comparison to those of the untransformed counterparts E32 and the conventional variety Yuexiangzhan during all of them were grown under a natural paddy field for two different cropping seasons of two consecutive years, according to the design of non-competition (monocultures) and competition (E121-2-1 or E122-2-9 mixtures with E32 and Yuexiangzhan) respectively. The results showed that the plant height, 1000-grain weight and number of spikelets per panicle of E121-2-1 and E122-2-9 under competitions were significantly lower than those under non-competitions in two years or one of two years, the competitiveness of agronomic traits of E121-2-1 and E122-2-9 were substantially inferior to that of E32 and Yuexiangzhan. The net replacement rates of E121-2-1 and E122-2-9 under competitions were decreased in two years, especially that of E121-2-1 decreased significantly in one of two years, but no significant differences were observed for the net replacement rates of E32 and Yuexiangzhan between competitions and non-competitions even though their net replacement rates increased or decreased according to different years. In contrast to E32 and Yuexiangzhan, E121-2-1 and E122-2-9 were statistically with lower rates of pollen germination, seed germinating energy, seed germination and volunteer in two years or one of two years, with longer periods of seed dormancy and with approximative abilities of seed bank persistence in two years. It was concluded that E121-2-1 and E122-2-9 had no advantages in ecological fitness, and they would not exceed their non-transgenic counterparts in survivability and sustainability of population under a natural conditions.