The origins of the Hutu, Tutsi, and Twa people is a major controversial issue in the histories of Rwanda and Burundi, as well as the Great Lakes region of Africa. The relationship between the three modern populations is thus, in many ways, derived from the perceived origins and claim to "Rwandan-ness". The largest conflicts related to this question were the Rwandan genocide, the Burundian genocide (Hutu and Tutsi), and the First and Second Congo Wars.
Ugandan scholar Mahmoud Mamdani identifies at least four distinct foundations for studies that support the "distinct difference between Hutu and Tutsi" school of thought: phenotype and genotype, cultural memory of inhabitants of Rwanda, archeology, and linguistics.
Most Tutsis and Hutus both carry the Haplogroup E1b1a paternal haplogroup which is common among Bantu and most other Niger-Congo-speaking populations.
Overview
When Europeans arrived in Rwanda to begin documenting traditions, Rwandan society consisted of three ethnicities that also serve as social castes. The largest group is the Hutu, consisting mostly of farmers. The second largest group is the Tutsi, mostly pastoralists, warriors and aristocrats. The smallest group is the Twa, which is a group of pygmy that hunt game to trade for agricultural products from the farmers. All three groups speak Kinyarwanda, which is a Bantu language.
There is disagreement as to when and how each group appeared in Rwanda. Some suggest the three groups diverged from each other while others suggest each group arriving in separate migration waves, first Twa, then Hutu, and finally Tutsi. In the separate arrival story, there is dispute in where the groups came from, when and how they arrived, and whether the arrival of some groups brought with them certain social development.
Hamitic hypothesis of Tutsi origin
The colonial scholars who found complex societies in sub-Saharan Africa developed the Hamitic hypothesis. The now rejected hypothesis posits that the Tutsi was a Hamitic race originated from the Horn of Africa that conquered Rwanda and brought civilization.
Migration hypothesis of Tutsi origin
Later scholars developed the migration hypothesis. While most supporters of the migration theory also support the idea that Tutsi came from the Horn of Africa, a later theory proposed that the Tutsi had instead migrated from nearby interior East Africa, and that the physical differences were the result of natural selection in an arid climate over millennia. Among the most detailed theories was one put forward by Jean Hiernaux, based on studies of blood factors and archeology. Noting the fossil record of a tall people with narrow facial features several thousand years ago in East Africa, including locations such as Gambles Cave in the Kenya Rift Valley and Olduvai Gorge in northern Tanzania, Hiernaux argues that while there was a migration, it was not as dramatic as some sources have proposed. He explicitly attacks the Hamitic theory that migrants from Ethiopia brought civilization to other Africans.
However, in light of recent genetic studies, Hiernaux's theory on the origin of Tutsis in East Africa appears doubtful. It has also been demonstrated that the Tutsis harbor little to no Northeastern African genetic influence on their paternal line. On the other hand, there is currently no mtDNA data available for the Tutsi, which might have helped shed light on their background.
One school of thought noted that the influx of pastoralists around the fifteenth century may have taken place over an extended period of time and been gradual and peaceful, rather than sudden and violent. The key distinction made was that migration was not the same as conquest. Other scholars delinked the arrival of Tutsi from the development of pastoralism and the beginning of the period of statebuilding. It appears clear that pastoralism was practiced in Rwanda prior to the fifteenth century immigration, while the dates of state formation and pastoralist influx do not entirely match. This argument thus attempts to play down the importance of the pastoralist migrations.