Domestication is the process in which preferred genetic changes in wild plants and animals have been selected by humans. In other words, domesticated plants have become adapted to being part of human-managed ecosystems. Asian cultivated rice, Oryza sativa L., is one of the most important crops in the world and is known to have been domesticated from its wild ancestor, O. rufipogon. Many morphological changes in cultivated rice have been beneficial to humans in terms of increased efficiency of cultivation and yield that supported the development of human civilisations. The genetic mechanisms of these changes have been extensively studied since rice genome sequences were determined, and based on genome analyses, the origin of rice has been widely discussed. Most of the domestication-related traits and genes are, however, often evaluated based on the genetic background of cultivated rice, leading to misinterpretation of rice domestication. Here, we review several genetic changes and discuss the importance of evaluating these traits in the wild rice genetic background to understand the process of rice domestication. In this review, we also provide a phenotypic evaluation of domestication-related traits.