Abstract:We studied the genetic difference between species in Alnus with different ploidies by using AFLP. Five AFLP primers produced 301 bands, of which 282 were polymorphic, accounting for 93.7%. The percentage of polymorphic bands of four population was 35.2% 72.4%, respectively, with an average percentage of 54.6%. The total population of genetic diversity Nei’s was 0.3043, and total Shannon polymorphism information was 0.4578. Among and within populations all had abundant genetic diversity, and the genetic difference interspecific was higher than that of intraspecific. By NJ cluster and PCOA, the closely related populations are geographically restricted and occur in proximity to each other.