The present work combines archaeology, historical analysis, and ethnography to examine historical continuities in village social organization and settlement patterns in southern Taiwan in the mid- to late second millennium a.d. The focus of the work is Kau-shi village, located in Mu-dan County, Pin-dong District, at the southern tip of Taiwan. Its residents belong to the Southern Pai-wan Group, one of Taiwan’s indigenous populations. Kau-shi people moved and established new settlements six times before they settled on the current village. Their oldest abandoned settlement, Saqacengalj, is located about 7 to 8 km from the current village, an archaeological site covering about 1.4 acres with more than 83 stone structures dated to 500–600 years b.p . (before present), known previously through mystical folktale and oral tradition, and only recently through archaeology. Archaeological mapping of site layout and structural features found that the Saqacengalj settlement shares certain characteristics with later Pai-wan settlements extending into the twentieth century. However, there are certain features distinctly Saqacengalj from these settlements. In addition, a significant percentage of the 83 structures at Saqacengalj have a unique arrangement of small structures within the larger structure not found in later villages. These initial archaeological analyses suggest significant historical changes in the cultural and social meaning of village settlement patterns of the Southern Pai-wan Group over this half-millennium.