Grain legumes of the Vigna genus are important crops in Asia, although their origins and history of domestication and cultivation are less known than that of rice and millet. Azuki (V. angularis var. angularis) is widely cultivated and consumed across East Asia, especially in China, Korea and Japan, which are considered as independent centres of azuki domestication. This study presents the first directly dated archaeobotanical record of V. angularis from prehistoric cultural layers at the Sanbaopi 5 archaeological site (23°07′03″N, 120°15′32″E, 3 m above sea level) located in the Tainan Science Park, south-western Taiwan. The archaeological dataset is compared with charred modern reference material and records from other prehistoric sites in East Asia and then discussed in context of cultivation and domestication. The obtained results suggest that V. angularis was used in the study area between the first half of the 1st millennium BCE (Wushantou phase) and 6th century CE (Niaosong phase) and that it was an important part of the diet of local populations. The younger specimens appear on average larger than the older ones. It is possibly that during this period the pulse underwent selection for size increase so that at least the specimens dating to the 6th century CE may be addressed as azuki (V. angularis var. angularis), the domesticated form of V. angularis var. nipponensis. This indicates that prehistoric Taiwan may have been an independent center of azuki cultivation/domestication in addition to the previously suggested regions. However, compared to evidence for azuki domestication in Japan, Korea and China, which dates to between ca. 4000 and 1000 BCE, the larger pulses from Taiwan appear quite late (about 4500–1500 years later). An alternative scenario to regional domestication is that azuki was introduced to the island by immigrating farmers or via good exchange across the Taiwan Strait.