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MicroRNAs (miRNAs) play vital roles in plant development and growth with negative regulation.Carya cathayensis (hickory) is an important species for dried nuts and oil, with high nutritional and economic value.To understand the roles of miRNAs involved in the hickory graft process, we constructed three small ribonucleic acid (RNA) libraries from hickory rootstock (2 years old) and scion (1 year old) of 0, 7, and 14 days postgraft.Sequences analysis of the three libraries identified 21 conserved miRNAs belonging to 13 families, 10 novel and 8 potential novel miRNA belonging to 15 families.Among these miRNAs, 12 miRNAs were differentially expressed during the graft process in hickory and most of them were downregulated.Quantitative real-time polymerase chain reaction (qRT-PCR) validated 14 miRNAs and their expression trends were similar to the results obtained by Soelxa sequencing.Further, a total of 89 target genes for conserved and 26 target genes for novel miRNAs were predicted.This study will help in understanding the roles and regulatory modes of miRNAs involvement in the hickory graft process.