microRNAs(miR NAs) are important post-transcriptional regulators of gene expression in plant abiotic stress responses. Ammopiptanthus mongolicus is a typical evergreen woody xerophyte, which makes it an ideal model system for studying drought tolerance in woody plants. The response of mi RNAs to drought stress is still unknown in this plant. In this research, we obtained 34 695 665 raw reads from two small RNA libraries constructed from control and drought-treated A. mongolicus seedlings by the Illumina deep sequencing technology. Length analysis revealed that reads of 20, 21, and 24 nucleotides accounted for the majority of the small RNAs in the two libraries. Sequence analyses identified 65 conserved mi RNA sequences from 190 members of 31 mi RNA families and 20 potential novel mi RNAs from 17 families that were differentially expressed between the two libraries. The expression patterns of 25 of these mi RNAs were significantly different in the two libraries, but only am-mi R4 a-c was downregulated during drought stress, the other 24 were upregulated. The expression trends determined by the Hi Seq sequencing and by q RT-PCR were similar. Furthermore, 35 target genes for the conserved mi RNA were markedly changed and 52 target genes for the potential novel mi RNAs were predicted and their functions were annotated by computational analysis. Our results provide new molecular evidence for understanding the molecular mechanisms of drought response and tolerance in A. mongolicus.