The morphological traits from Gaozhou wild rice populations in Guangdong Province were collected and clustered by using a variable-average method. The results indicated that there were abundant variations of traits in the natural populations, especially significant differences in vegetative organs and seed production potentiality among the populations of Daling village, Fushi village, Boshui village and Pengshan village. These differences may be due to the different water stability, the water line and disturbance strength among the populations.