Dental morphological characteristics of the early modern population (c. 17–19th century AD) of Okinawa Island, Nansei Islands, were investigated to clarify their genealogical characteristics. We observed and classified 25 nonmetric traits of tooth crowns and roots from human remains (106 individuals) excavated from tombs of the early modern period in Okuma, Ginowan City, Okinawa. The incidences of these traits were compared with the incidences in the populations of the other Nansei Islands, of Japan, and of Asia overall. Univariate analysis of each trait and multivariate biological distance analysis based on the frequencies of the traits showed that the Okinawa population in the early modern period more closely resembled the migrant Yayoi populations than it did the native Jomon populations. It is difficult to support the “Ainu-Ryukyu common origin theory” with regard to the early modern population in Okinawa without some modification of the theory, as well as the modern populations in Tanegashima and Okinawa Island. The geographical cline in the modern period from the northern Kyushu to the Okinawa Island via Tanegashima was confirmed in this analysis. Considering the major temporal changes in northern Kyushu and Tanegashima in addition to the geographical cline, the southward gene flow of the migrant Yayoi elements from northern Kyushu to the central Nansei Islands via the northeast end of the Nansei Islands is suggested. In addition, this study detected some temporal changes from the early modern to the modern period in Okinawa Island. Although the minor temporal change may be attributed to some genetic drift, gene flow from the Japanese main islands or China might be considered one of the causes of the change. Copyright © 2010 John Wiley & Sons, Ltd.