We study the ancient genetic variation of humans in two regions of Peru, the eastern slopes of the northern Peruvian Andes where the Chachapoya society dominated the area prior to Inca conquest and the southern Peruvian coast where various cultures, such as the Chiribaya, existed. Another line of research focuses on the study of persistent human DNA viruses, their distribution in several organic tissues, their diversity and particularly their evolution in the context of these two environmental settings where different selective pressures may have operated. Our datasets come from pre-Inca periods, Inca as well as peri- and post European contact. We interpret our findings in conjunction with the complex histories provided by other disciplines such as archaeology and ethnohistory while also incorporating radiocarbon dates and dietary stable isotope data.