Camellia japonica L. usually blooms red flower in winter in Jeju island, Korea, considered a species which should not be planted in the garden. Here, we completed chloroplast genome of C. japonica isolated in Seogwang-ri, Jeju island for comparing that isolated in Wimi-ri, Jeju island. Its length is 156,971 bp long and has four subregions: 86,673 bp of large single copy (LSC) and 18,394 bp of small single copy (SSC) regions are separated by 25,952 bp of inverted repeat (IR) regions including 135 genes (91 protein-coding genes, eight rRNAs, and 36 tRNAs). Its overall GC content is 37.3\% and those in the LSC, SSC, and IR regions are 35.3\%, 30.5\%, and 43.0\%, respectively. One insertion and one deletion are identified between chloroplast genomes of Soyeonpyeong island and Seogwang-ri, even though both places are far enough (>450 km). Twenty-five single nucleotide polymorphisms (SNPs) are identified within two Jeju island chloroplast genomes, presenting that C. japonica tree in Wimi-ri is genetically far from the two chloroplast genomes. Trees also show that genetic diversity of C. japonica is lower than that of C. sinensis.