Abstract:Based on the analysis of miRNAs omics in longan ECs, we selected the differentially expressed miR396a3p_2 and miR396b5p for further analysis and verification, which play a key role in the regulatory pathway about effect of blue light on longan. We analyzed the phylogenetic tree of precursor and mature sequences, the secondary structure and cisacting element of precursor, the prediction of target genes, as well as expression patterns responding to blue light of miR396 in this study. These results showed that: (1) the miR396 mature sequences from 5p arm were highly conserved and from 3p arm were quite specific. The stem sequence was more conserved than loop sequence, and the miRNA from 5p arm sequence was more conserved than that from the 3p arm. (2) They both contain many lightresponsive elements, hormoneresponsive elements, and biotic and abiotic stress responsive elements, which might play a regulatory role in response to blue light through these ciselements. Their targets responding to blue light both contain growthregulating factor 2 (GRF2), LRR receptorlike serine/threonineprotein kinase (FLS2), ethyleneinsensitive protein 3 (EIN3) and DNAdirected RNA polymerase subunit alpha (ropA) etc. Realtime quantitative PCR showed that there were differences in the expression patterns of miR396a3p_2 and miR396b5p under different light qualities. The expression trends of miR396b5p and its targets presented negative correlation under the blue light conditions with different light intensities, while miR396a3p_2 was not negatively correlated with rpoA. This might be the reason that other miR396 family members or miRNAs were also involved in this process to achieve regulation of target gene transcription levels.