Nitrate and ammonium are two major nitrogen(N) sources for higher plants,but they differ in utilization and signaling.Micro RNAs(mi RNAs) play an essential role in N signal transduction;however,knowledge remains limited about the regulatory role of mi RNAs responsive to different N sources,especially in crop plants.To get global overview on mi RNAs involved in N response in rice,we performed high-throughput small RNA-sequencing under different nitrate and ammonium treatments.The results demonstrated that only 16 and 11 mi RNAs were significantly induced by nitrate and ammonium under short-term treatment,respectively.However,60 differentially expressed mi RNAs were found between nitrate and ammonium under long-term cultivation.These results suggested that mi RNA response greatly differentiates between nitrate and ammonium treatments.Furthermore,44 mi RNAs were found to be differentially expressed between high-and low-N conditions.Our study reveals comprehensive expression profiling of mi RNAs responsive to different N sources and different N treatments,which advances our understanding on the regulation of different N signaling and homeostasis mediated by mi RNAs. Nitrate and ammonium are two major nitrogen (N) sources for higher plants, but differ between utilization and signaling. Micro RNAs (mi RNAs) play an essential role in N signal transduction; however, knowledge remains limited about the regulatory role of mi RNAs responsive to different N sources, especially in crop plants. To get global overview on miRNAs involved in N response in rice, we performed high-throughput small RNA-sequencing under different nitrate and ammonium treatments. the results that only that 16 and 11 mi RNAs were significantly induced by nitrate and ammonium under short-term treatment, respectively. However, 60 differentially expressed miRNAs were found between nitrate and ammonium under long-term cultivation. These results suggest that miRNA response greatly differentiates between nitrate and ammonium treatments. Furthermore, 44 mi RNAs were found to be differentially expressed between high-and low-N conditions. Our study reveals comprehensive expression profiling of m i RNAs responsive to different N sources and different N treatments, which advances our understanding on the regulation of different N signaling and homeostasis mediated by mi RNAs.