Archaeological research in the Yaeyama Islands, southern Japan, has a hundred year old history, yet little of it is known to those archaeologists working outside the immediate area. This area is of importance to those working in Southeast Asia and the Pacific as the colonisation of the Yaeyama Islands allows a closer assessment of the nature and timing of Austronesian movement out of Taiwan. This paper will examine the colonisation of the Yaeyama Islands and its archaeological signature, Shimotabaru pottery, by first reviewing the archaeological developments of this island group, followed by an examination of the timing of colonisation and the nature of Shimotabaru pottery production. It will be argued that the early occupation in the Yaeyama Islands characterised by Shimotabaru pottery is the signature of Austronesian colonisation from Taiwan, from between 4500 and 3900 years ago. Yet the colonising signature in the Yaeyama Islands is of a different character to the Austronesian presence in the islands south of Taiwan. This suggests that the nature of Austronesian expansion in general was more complex than is proposed in the prevailing model.