Although the social organization of many of the present-day pueblos of the American Southwest is well-described in the anthropological literature, many aspects of prehistoric Puebloan social organization have received limited attention since initial investigations of postmarital residence in the 1960s and 1970s. This paper examines postmarital residence at the Chaco Canyon great house of Pueblo Bonito, using biological data. Our findings are inconsistent with the previously well-accepted hypothesis that the Pueblo II and Pueblo III occupants of the San Juan Basin conformed to a socially prescribed pattern of matrilocal residence with matrilineal descent. Univariate variance differences for nine craniometric variables indicate a pattern of increased female variability consistent with patrilocal/bilocal residence. The results of multivariate determinant ratio analyses are in agreement with the univariate results, suggesting the possibility of a patrilocal or bilocal residence preference at Pueblo Bonito. These findings are inconsistent with the notion that the female-based system of matrilocal residence with matrilineal descent observed among the present-day Western Pueblos was the ancestral Anasazi condition. Am J Phys Anthropol 120:1–15, 2003. © 2003 Wiley-Liss, Inc.