Solution culture experiment was carried out to study the effects of different exogenous iron concentrations on seedling growth, contents of ammonium, iron and potassium ions of two rice genotypes – Japonica (Zhonghua 11) and Indica (Yangdao 6th) under different nitrogen sources. Results showed that the increase of exogenous iron level significantly alleviated ammonium inhibition on root growth of Japonica, but no effect on that of Indica. The increase of exogenous iron concentration significantly increased iron contents in roots of two rice varieties, and significantly reduced the contents of ammonium ion in roots of two rice varieties under the condition of ammonium nitrogen, and change trends were similar between the two genotypes. Under the co-stress of ammonium and iron, potassium contents in roots of two genotypes significantly reduced, and the change trends were similar between the two genotypes. Japonica was more resistant to iron toxicity, and the reduction of potassium content in roots of Indica was more sensitive to iron toxicity under nitrate-nitrogen. These results proved that the alleviating effects of increasing exogenous iron concentration on ammonium toxicity of roots in different rice ecotypes were different, possibly associated with the resistance of iron toxicity.