Abstract:The finger map of longan (Dimdcarpus longan Lour. ‘Honghezi’) cotyledon embryo RNA was established by cDNA-AFLP, which extracted from thirty-five-day (early) and fifty-day (late) cotyledon embryos after anthesis, respectively. There were 41 differential fragments cloned and sequence analysed, in which 21 differential expression fragments had high homology with some known genes, the function mainly involved in the abaxial polarity of lateral organ, glycolysis, energy metabolism, ion transport, cell wall elongation, cell cycle regulation, RNA transcription, RNA translation and regulation, protein phosphorylation regulation and protein degradation, signal transduction and so on. While the others had low or no homology with known genes.