in diverse biological and metabolic processes in plant development.Since the first plant miRNAs were discovered in Arabidopsis,both experimental methods and computational approaches have been adopted to identify miRNAs in many other model species and angiosperms plants,but with only a few researches on woody trees especially gymnosperms.Up to date,there is no miRNA found in Ginkgo biloba and little is known about miRNAs involved in the key stage during it’s partly epiphyllous ovules germination.In this research,the next generation high through-put Solexa sequencing technology combing with bioinformatics analysis were employed to sequence and identify conserved and species- specific Ginkgo biloba var.epiphylla miRNAs in the epiphyllous ovule leaves and normal leaves.In total 83 conserved miRNAs belonging to 29 miRNA families including 1 putative gymnosperm-sepcific miRNA family (miR1314) were identified.Besides 3 novel miRNA families were also identified.Further differential expression analysis showed that 17 miRNAs showed extremely significant difference in the two samples.The putative miRNA target genes of miRNAs were involved in pathways associated with plant leaf morphogenesis,vegetative phase change and reproductive physiology,etc..The patterns of miRNA expression differed significantly between epiphyllous ovule leaves and normal leaves,which provide important information on epiphyllous ovule phenomenon.Diverse expressed miRNAs in different time and tissues combing with other small RNAs may play a key regulatory role in Ginkgo biloba var.epiphylla development.In the future,it is necessary to do experiment on some miRNAs and their targets these may play important role in Ginkgo biloba var.epiphylla,with the purpose of investigating the regulation mechanism about the epiphyllous ovule phenomenon.