miRNAs are endogenous regulatory factors that play pivotal roles in post-transcriptional regulation. However, their specific roles in early somatic embryogenesis (SE) remain unclear. Study of the SE system is fundamental for clarifying the molecular mechanisms in Dimocarpus longan. We identified 289 known miRNAs from 106 different miRNA families and 1087 novel miRNAs during early longan SE, including embryogenic callus (EC), incomplete pro-embryogenic culture (ICpEC), globular embryo (GE), and non-embryogenic callus (NEC). The abundances of known miRNAs were concentrated in GE. The differentially expression (DE) miRNAs showed five expression patterns during early SE. Largely miRNAs were expressed highly and specially in EC, ICpEC, and GE, respectively. Some miRNAs and putative target genes were enriched in lignin metabolism. Most potential targets were related to the pathways of plant hormone signal transduction, alternative splicing, tyrosine metabolism and sulfur metabolism in early longan SE. The regulatory relationships between dlo-miR166a-3p and DlHD-zip8, dlo-miR397a and DlLAC7, dlo-miR408-3p and DlLAC12 were confirmed by RNA ligase-mediated rapid amplification of cDNA ends. The expression patterns of eight DE miRNAs detected by qRT-PCR were consistent with RNA-seq. Finally, the miRNA regulatory network in early SE was constructed, which provided new insight into molecular mechanism of early SE in longan.Plant somatic embryogenesis (SE) is physiologically and morphologically similar to that of zygotic embryos. Therefore, SE is usually used as a model system for studying embryonic development in higher plants. Previously study demonstrated that transcription factors (TFs) regulated embryogenic transformation in SE 1 ; this TFs included BABY BOOM (BBM), AGAMOUS-LIKE15 (AGL15), LEC2 and SERK, which functioned in the process of cell division and differentiation in embryonic development 2 . miRNAs are a kind of small endogenous RNAs of 18-24nt in length, which mainly recognize the complementary binding sites of their target mRNAs. miRNAs were transcribed by RNA polymerase II (Pol II). miRNAs could mediate mRNA cleavage and inhibiting translation at transcriptional or post-transcriptional level in eukaryotes 3,4 . Over the past decade, miRNAs have been reported to be involved in a broad range of metabolic and physiological processes in plants, such as plant growth, development and responses to stresses. However, the regulation of miRNA of plant SE was still unclear.The miRNA regulatory pathway is particularly important in plant growth and development, hormone regulation, organ differentiation, alternative splicing and secondary metabolite accumulation 5-7 . The SE could be influenced by epigenetics in some plant 8 . For instance, expression levels of miR171, 159, 169 and 172 affected in the embryogenic potency of Larix gmelini 9 , these particular miRNAs targeted to multifunctional TFs and participated in ABA signal transduction, growth and development, and stress response. In Citrus sinensis (L.), miR156, 168 an...