Abstract: cDNA-AFLP technology was applied to identify differentially expressed genes between normal and abortive longan(Dimocarpus longan Lour.) seeds.Transcript-derived fragments(TDFs) identified as differentially expressed genes were eluted,cloned,sequenced and compared with the database using BLAST at NCBI.The results showed that among 11 sequenced fragments,three TDFs presented similarity with Ca²⁺-ATPase,cellulase,and plastidic ATP/ADP transporter,respectively,whose up-regulation or down-regulation expression might influence several important metabolic pathways in developing seeds and led to seed abortion.Four TDFs were similar with hypothetical protein,while the other four TDFs did not match with known proteins in the protein database,while sequence alignment from the DNA database also showed higher E-values,indicating they were non-homologous genes.