Surnames provide a useful method to study the structure of human populations for which biological data are not available. The isonymic method has had multiple applications, but difficulties emerge when dealing with groups where extramarital reproduction is common and the sample size is small, and even more so when only paternal surnames are taken into account. Therefore, it could be of interest to retain female surnames, including those of unmarried mothers. This study was carried out using all birth records from an Argentinian population in the colonial period, which was characterized by the presence of different ethno-social groups (Spanish, Indian and ‘Mestizo’ or mixed Spanish–Indian) and various reproductive patterns regarding legitimacy. Coefficient of relationship by isonymy (Ri) kinship matrices between geographical populations were obtained, and the results derived from sets of surnames (paternal, maternal of legitimate and illegitimate children, and all surnames in the registers) compared. The results show similar surname distribution regardless of the set of surnames and group considered. Kinship Ri matrices using paternal surnames, maternal surnames of legitimate children, maternal surnames of illegitimate children, and the set of whole surnames showed the same relationships among populations, indicating a similar pattern for Spanish, Indian and Mixed ethno-social groups. Mantel test correlation between all pairs of matrices was significant in all different ethno-social groups. The results suggest that in populations with high illegitimacy, such as that studied here, it is possible to include maternal surnames, even corresponding to single mothers, in order to consider total reproduction and therefore maximize sample size.