During the 19th century, scholars developed an interest in physical ethnography as a discipline for investigating the nation’s ethnogenesis. National-liberal ideology, combined with the impact of Positivism, helped create an ethnic-deterministic explanatory model for the nation’s singularity. In 1894 Teófilo Braga proposed an ethnogenesis based on the idea that, since prehistory, the peoples from the Iberian peninsula had been a mix between Indo-European and north African ethnic groups. During the Middle Ages, a mix between the Islamic occupiers and the Iberian population (which by then was the fusion of Celtiberic, Roman and Germanic populations) resulted in the emergence of the Moçarabes, an ethnic group which constitued the roots of the Portuguese people. In 1933, Martins Sarmento derived the Portuguese nation from Iron-Age Lusitanos, allegedly a pre-Celtic Aryan settler stratum. Craniology was called into play in the 1910s to link the dolichocephaly of the Portuguese population to these Lusitanos, thus extricating the Portuguese ethnogenetic narrative from its north African entanglements. Physical ethnography was also used to study regional identities, e.g. the singularity of the population from São Miguel (Azores) as studied by Arruda Furtado in 1884. In fact, the empirical data of physical ethnography was drawn upon in different disciplines, including palaeontology and colonial anthropology.

Physical ethnography was developed at the Comissão Geológica do Reino. It researched prehistoric sites not only geologically, but also, if ossified human remains were present, anthropologically, as part of the discussion on the antiquity of man in the Portuguese territory that had got underway in the 1860s. In 1871-73, Carlos Ribeiro hypothesized the presence of tertiary hominids, recording an association of flint tools to tertiary deposits at the Ota valley. This palaeontological research fed into a study of national origins: the people, language and territory of Portugal, as conducted by José Leite de Vasconcellos, at Lisbon’s Museu Ethnografico Português and in the Sociedade Carlos Ribeiro, as well as in the Porto-based journal Portugalya – materiaes para o estudo do povo português; and by Possidónio da Silva in Lisbon’s Associação dos Architectos Civis e Archeólogos Portugueses.

From the mid-1870s, pioneering work was done by the physician Ferraz de Macedo, who formulated evolutionary theories, introduced measurement instruments, collated data coming from living and dead samples, introduced the use of statistical analysis, and helped create large osteological collections. These innovations enabled him to create osteometric tables and reference patterns. These were used in turn as indices for studying fluctuations in the general state of health in the population, with eugenicist implications and physical criminology.

Physical ethnography was first institutionalized as a discipline at the University of Coimbra, in 1855, when a chair of anthropology, human palaeontology and prehistoric archaeology was created for Bernardino Machado. Machado also reorganized Coimbra’s Natural History Museum, enlarging the anthropology section with osteological collections (both from the mainland and from the colonies); he was succeeded by his pupil Eusébio Tamagnini, who was appointed to the chair of anthropology (Faculty of Sciences) in 1910 and to the chair of ethnology (Faculty of Humanities) in 1912. In 1914, the department started the journal Contribuições para o Estudo da Antropologia Portuguesa. Research in Coimbra provided data on popular health and other statistics, which allowed the government to rank the place of the Portuguese people within the European races and to underpin its supremacy in relation to the colonies.

After the 1884-85 Berlin Conference regulated the European scramble for African colonies, colonial anthropology became an important tool for colonial exploration; witness the creation of the Sociedade de Geografia de Lisboa and the expeditions of Brito Capelo, Serpa Pinto and Roberto Ivens, aimed at reinforcing the Portuguese presence in the colonial territories. It was also in this context that, in a military expedition to the province of Goa (1895-96), Fonseca Cardoso developed an anthropological study of the Indian population of the Satary region. Colonial anthropology subsequently obtained a strong institutional presence at the University of Porto, which received substantial funding for its research under the Salazar dictatorship. In the 1930s and 1940s, the state promoted a set of anthropological missions, whose wide-ranging agenda included the ethnographic study of colonial populations. Mendes Corrêa, professor at Porto and a founder of the Sociedade Portuguesa de Antropologia e Etnologia, was a central figure in these missions.