Abstract:We analyzed the genetic relationships of 17 Alnus, identified the uncertain species by AFLP markers and morphology data, and used UPGMA in clustering analysis. Seven primers were selected to conduct AFLP-PCR, and 369 DNA bands were obtained including 346 bands ofpolymorphism with93.77% of polymorphic bands. All these plants could be divided into four groups by AFLP cluster analysis: the first group was consisted of A.japonica;the second group was consisted of A.viridis, A.cordata, A.glutinosa, uncertain species, A.cremastogyne, A.trabeculosa, A.incana ssp.rugosa, A.hirsuta, A.formosana, A.firma and A.sinuata; the third group was consisted of A.incana, A.rubra and A.tenifolia; the fourth group was consisted of A.nitida and A.nepalensis. All these plants could be divided into three groups by morphology data: A.cordatawas the first group; the second group was consisted of A.japonica, A.formosana, A.nitida, A.hirsuta, A.trabeculosa; the third group was consisted of A.nepalensis, A.incana, uncertain species, A.incana ssp.rugosa, A.rubra, A.glutinosa, A.viridis, A.fima, A.tenifolia, A.sinuata and A.cremastogyne. The uncertain species was A.glutinosaby morphological and AFLP analysis.The results of morphological cluster analysis and AFLP cluster analysis were similar, but also had some difference, that is, Alnus hadvarious genetic background, and there were some differencesbetween the status of molecular and morphological classification between Alnus species.