Camellia japonica, an evergreen ornamental plant in the Theaceae family, has a natural range that is now shrinking. This is evident by the fact that the species is on the verge of extinction in Laoshan Mountain (Qingdao), the northernmost area of China known to have a natural population of C. japonica. Little is known about the genetic diversity and relationships among cultivated and wild C. japonica populations. One hundred and eighty samples of six C. japonica populations were tested for genetic diversity with simple sequence repeat (SSR) markers; these included three cultivated populations, two natural populations in Qingdao, and one natural population in Daqingshan. The average values of polymorphism information content (PIC), expected heterozygosity (He), and Shannon’s information index (I) were 0.5849, 0.6385 and 1.3170, respectively, indicating that C. japonica has a high genetic diversity. The genetic diversities of the six populations in rank order were as follows: Daqingshan > Zhongshan Park > Changmenyan Island > Daguan Island > Botanical Garden > May Fourth Square. The geographical isolation of the islands had no significant influence on the genetic diversity of C. japonica. Clustering results showed that the six C. japonica populations could be grouped into three categories, and most populations were clustered according to their geographical origin and genetic background. These results also reconfirmed that the C. japonica (Naidong) population in Qingdao originated from Changmenyan Island. Genetic variation was highest within populations (89%), indicating that C. japonica can be protected at the population level. These findings will prove useful for the genetic analysis, protection, and horticultural use of C. japonica.