Crop domestication can serve as a model of plant evolutionary processes. It involves a series of selection events from standing natural variation and newly occurring mutations and combinations of mutations as a result of natural crossings in populations during local adaptation and propagation of plant lines to other cultivation areas. Our earlier identification of three functional nucleotide polymorphisms (FNPs) of distinct genes involved in the rice domestication process led us to propose a model of the japonica rice domestication process. Here, we examined three more FNPs in two domestication-related genes involved in pigment synthesis during the development of seed pericarp color (Rc and Rd) in 91 landraces (and some modern cultivars) of japonica rice collected from throughout the area of distribution of rice. These polymorphisms were assigned by using genome-wide patterns of restriction fragment length polymorphisms (RFLPs) and the local origins of the landraces. The results led us to infer the process of japonica rice domestication in more detail and propose a more refined model of the japonica domestication process. In this model, the critical role of the Rc FNP at an early step of the domestication process was highlighted. Independent artificial selections of two defective Rd alleles were found, suggesting a role for Rd other than in pigment synthesis during rice domestication.