With the architecture of prehistoric sites and ancient civilizations constantly requiring new methodologies and forms of analysis, a new field of research the Archaeology of Architecture or ‘Archaeotecture’ has been designed to merge theory and method for that purpose. It combines aspects of ethnography, anthropology, archaeology and architecture to understand the material context of human social relations, culture and production as seen via architecture through time. Similarities have been drawn between prehistoric architecture and contemporary vernacular architecture of hunter-gatherer societies. This paper takes advantage of these similarities by employing methods used in ‘archaeotecture’ to ascertain cross-spatial and cross-temporal variations in the vernacular architecture of Ijo migrant fishermen in Nigeria. The Principal Co-ordinate Analysis which is a quantitative technique adopted from archaeology was applied in the analysis of architectural data to ascertain variations in vernacular built forms. The results indicated the existence of variations as well as the cultural transmission mechanisms that may have influenced these variations. The paper concludes by discussing and recommending the use of interdisciplinary cross-pollination of methods in examining variations in both vernacular and contemporary architectural studies