SAUR (small auxinup RNA) genes are a class of early response genes to growth hormone, which are closely related to plant growth and development. In order to reveal the regulatory roles of SAUR63 and SAUR64 during the early somatic embryogenesis of longan, we used TAcloning to obtain the coding sequences of SAUR63 and SAUR64, and then inserted into the vector for subcellular localization analysis, qRT PCR expression analysis and fluorescence in situ hybridization analysis. The results showed that: (1) the sequence length of SAUR63 and SAUR64 in longan were 386 and 312 bp, respectively. Phylogenetic tree analysis showed that SAUR63 and SAUR64 were highly homologous to Arabidopsis thaliana. Subcellular localization results showed that SAUR63 was localized in the nucleus and extracellular matrix, and SAUR64 was localized in the chloroplast. (2) SAUR63 and SAUR64 were both predicted to be as target genes of LTCONS_00038949, LTCONS_00038950 and LTCONS_00038952 (lnc38949, lnc38950 and lnc38952). (3) The results of qRT PCR showed that SAUR63, SAUR64 and three lncRNAs were highly expressed at the stage of incomplete embryonic compact structure. SAUR63 and three lncRNAs were upregulated under 100 and 500 μmol·L^-1 gibberellin (GA₃) treatment, and the expression level reached the peak under 500 μmol·L^-1 GA₃ treatment. SAUR63, SAUR64, lnc38949 and lnc38950 were significantly induced at 35 ℃, while lnc38950 was inhibited. In addition, SAUR63, SAUR64 and the three lncRNAs were also response to SA, MeJA, salt stress and drought stress. (4) Fluorescence in situ hybridization result showed that both SAUR63 and lnc38949 were not localized in the specific site of the zygotic embryo, and the expression of lnc38949 was higher than SAUR63. The results showed that SAUR63 and SAUR64 may be regulated by lncRNAs and participate in the regulation of longan early somatic embryogenesis.