Schima wallichii (DC.) Korth. (Theaceae) is a common canopy trees distributing from tropical to subtropical areas in East Himalaya, Southeast Asia and East Asia. Although many seedlings of S. wallichii are planted to rehabilitate degraded natural forests in West Java, there are few studies of its genetic differentiation and the risk of plantation to disturb the genetic structure. There is also debate whether Schima trees in Java and Ryukyu are in a same species or not. This study was initiated to remedy these deficits by screening genetic differentiations using inter simple sequence repeats (ISSR) analysis with eight primers. Leaves were sampled from 250 trees at seven sites in the Mt. Halimun-Salak and Mt. Gede-Pangrango National Parks in West Java, and 32 trees at four sites on Amami Islands of the middle Ryukyu Archipelago. Principal component analysis (PCA) of 155 polymorphic bands from 282 trees showed that Schima in both regions had high level of genetic variation within a given site. Genetic differentiations among sites in a region was low though some sites had a significantly different mean of PCA scores from other sites. The introduction of seedlings from other sites in the same region may have a low risk of genetic pollution though many mother trees should be prepared to maintain the variation in a site. The first scores of PCA discriminated trees of Java from those of Amami without overlap. Schima in West Java and Amami are probably different subspecies or species from each other.