 This study discovered 10 new potential micro-RNAs, myrnas, and 42 highly conserved myrna families in trifoliate orange, citrus trifoliatae, an important rootstock of citrus. The myrnas were identified through deep sequencing of short RNAs from trifoliate orange flowers and fruits. Additionally, for target genes, including one encoding IRX-12, copper ion binding, oxido reductase, and three genes encoding NBLR disease resistance proteins were experimentally verified by detecting the mi-RNA-mediated mi-RNA cleavage in trifoliate orange. This study provides evidence that specific myrnas exist in trifoliate orange and may play an important role in citrus growth, development, and response to disease. This article was authored by Yuhua Ping, Cori and Nicholas, Zhong Chongqing, and others.