Structures and properties of starches isolated from Japanese rice and different botanical sources were investigated. Amylopectin unit chain-length distributions were analyzed using HPLC and HPAEC-PAD for comparing the distributions of unit chains of isoamylase-debranched amylopectins. Thermal properties were measured by DSC. It was found that there were at least five groups of Japanese rice amylopectins having different unit-chain distributions. The four kinds of starches (Akenohoshi, Haiminori, Tashukei 431, and Kenkei 2064) had the amylopectins of long chain-length compared with the other rice starches. It was observed that the gelatinization temperature of their four native starches were higher and the enthalpy change (•H) of gelatinization of their four retrograded starches showed larger than the other rice starches. In the starches of different botanical sources, the ratios of unit chains of DP6-12 (Fr.A) of amylopectins of quinoa, barley, buckwheat, Japanese radish, and tulip were higher, and the gelatinization temperatures were lower than the values of other starches. The ratios of Fr.A of amylomaize V and VII were lower, and the gelatinization temperatures were higher than the respective values of other starches. There were highly negative relationships between the ratio of short unit chain-length in amylopectin and gelatinization temperature.