The genus Dipteronia Oliv.(Aceraceae) is endemic in China which consists of two species:D.sinensis Oliv.and D.dyerana Henry.Dipteronia is one of the woody relic genera in the floristic regions of the northern temperate zone.In this study,we carried out a comparative study of D.sinensis Oliv.and D.dyerana Henry.to explore their degree of differentiation between two species from the aspects of morphology,molecular genetics and gene sequence analysis.(1)Morphological studies indicated that the presence of two species in morphological characters have significant differences.(2)Molecular genetic studies based on the AFLP of genomic DNA markers were also used to analyze the two species.And whether they are in species level or group level,the results showed that there was extremely significant genetic differentiation between the two species(Φ_ST=0.390 4).The level of genetic variation and genetic diversity of the two species have distinct differences(D.sinensis Oliv.＞D.dyerana Henry).(3)We also downloaded several chloroplast genes (psbM-trnD,trnD-trnT,trnL,trnL-trnF,rpl16) and nuclear gene sequences of ITS (ITS1,5.8SRNA,ITS2) of two known species from GenBank to analyze and compare their differentiation.t-test showed a significant difference between the two species occurred in chloroplast gene sequences.Hence,the results of the present study showed that the D.sinensis Oliv.and D.dyerana Henry have a extremely significant differentiation.And we infer the main reasons of the significant differentiation between the two species attributed to the long-term geographic isolation between them.