Camellia japonica is an important horticultural species, widely distributed in East-Asia. Four populations of C. japonica were analyzed by ISSR markers to detect the genetic diversity. Twenty primers with discernible DNA bands markers were applied. The percentage of polymorphic bands, Nei’s gene diversity and Shannon’s Information Index were 64.06%, 0.2390 and 0.3548, respectively, indicated that the genetic diversity of C. japonica populations was relatively high. The value of differentiation (Gst = 0.2241) affirmed that C. japonica had high genetic differentiation among populations. The effect of geographical isolation had great influences and significant correlation was found between genetic distance and geographic distance (r = 0.9653, P<0.05). UPGMA analysis revealed that populations on the same isalnd had a closer relationship. In order to maintain genetic diversity and resource utilization of C. japonica, management strategies were proposed that natural population should be protected in situ from human disturbance to facilitate it s natural generation.