In Japan, Camellia japonica and Camellia rusticana are naturally distributed. Despite differences in their habitats and morphologies, they have been classified by various researchers as either varieties, sub-species, or species. The taxonomic position of C. japonica and C. rusticana remain unclear because morphological comparisons have been restricted to limited areas and quantitative data are scarce. C. rusticana grows in snowy places, unlike C. japonica. While C. japonica displays ornithophily, C. rusticana displays entomophily. Both species have adapted to different growing environments and pollinators, which have altered the morphology of flowers and leaves. We therefore quantitatively estimated the differentiation between these two taxa by comparing the morphologies of leaf hypodermis, flower form, petal color, and filament color in twenty populations. Our findings allowed us to differentiate these two species by the presence or absence of a leaf hypodermis. We also discovered an intermediate type of leaf hypodermis, which might also be caused by hybridization. Principal component analysis (PCA) indicated that the flower morphologies between these species were significantly different. The petal and filament colors were also significantly different. Our quantitative analysis suggests that speciation caused by differences in both pollinators and environment is one of the factors involved in this group. These findings in C. japonica and C. rusticana help to explain speciation processes for other species as well.