The Hutu are believed to have first emigrated to the Great Lake region from Central Africa in the great Bantu expansion. Various theories have emerged to explain the purported physical differences between them and their fellow Bantu-speaking neighbors, the Tutsi. The Tutsi were pastoralists and are believed to have established aristocratic control over the sedentary Hutu and Twa. Through intermarriage with the Hutu, the Tutsi were gradually assimilated culturally, linguistically and racially.

Others suggest that the two groups are related but not identical, and that differences between them were exacerbated by Europeans, or by a gradual, natural split, as those who owned cattle became known as Tutsi and those who did not became Hutu. Mahmood Mamdani states that the Belgian colonial power designated people as Tutsi or Hutu on the basis of cattle ownership, physical measurements and church records.

The debate over the ethnic origins of the Hutu and Tutsi within Rwandan politics predates the Rwandan genocide, and continues to the present day, with the government of Rwanda no longer using the distinction.