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Coefficients of relationship by isonymy, based on the frequency of common surnames, were used to estimate the biological affinity between (Rib) and within (Riw) 16 Sardinian villages in the periods 1825–1849, 1875–1899, and 1925–1949. The database for the surname analysis consisted of 13,515 marriages registered in the parishes of villages, all belonging to the Sardinian linguistic area. The values of Rib and Riw tend to decrease in time. In all three periods, the Rib values generally decrease as the geographical distance between villages increases. The negative values of the Bravais-Pearson coefficient of correlation between the matrix of Rib values and the matrices of geographical distances (calculated both in a straight line and from road distances) are significant for each period (modified Mantel test), with slightly higher correlation coefficients for road distances. Moreover, the plots of isonymic relationships obtained by nonmetric multidimensional scaling for 1825–1849 and 1925–1949 show that the biological relationships between neighboring villages increase in the latter period. The positive values of the Bravais-Pearson coefficients of correlation between Riw and altitude are significant in all three periods, while the correlation between Riw and population size is not significant, even when altitude is controlled for. Since altitude is considered an indicator of isolation, the results obtained with the coefficient of relationship by isonymy within villages also support the isolation-by-distance model. Rib values provided a reliable picture of the biological relationships between 16 Sardinian villages, while Riw values illustrated the biological affinity within the communities for a period of 100 years, from 1825–1849 to 1925–1949. Am. J. Hum. Biol. 18:621–629, 2006. © 2006 Wiley-Liss, Inc.