His primary research focus has been on the Zapotec civilization of central Mexico and Oaxaca, and he is the author of half a dozen monographs on the subject.
In addition to his research on the Zapotec, Whitecotton has made contributions in historical ethnography, the study of political economies and the effects of globalization trends on local cultures.
He has also investigated evidence for pre-Columbian contacts and trade between Mesoamerica and cultures in the American Southwest, and conducted ethnographical research of the Hispanos in New Mexico.
Since then he has retained a position at OU as Professor Emeritus of Anthropology and Liberal Studies, and continued to be active in research publications and conferences.
After his formal retirement in 1999 Whitecotton spent two academic years (2003 and 2005) as a visiting professor in anthropology at North Carolina's Wake Forest University.