After amplification of 15 accessions of Ae.longissima by 70 selected primers,766 bands were obtained,85% of which (651) showed polymorphism.However, about 38% (253) of the bands with polymorphism were presented in 3 samples.The above result revealed that Ae.longissima was composed of two populations with less variation within each population and greater variation between the two populations.The results of RAPD showed that the genetic distance between two populations was three times of that within population.With consideration on the variation of morphology and seed setting rate in crossing with wheat,we suggested that Ae.longissima be divided into two sub-species.