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In his book, "When Victims Become Killers," Mahmood Mamdani charts some basic biological/physical differences between these two groups that co-occupy Rwanda. For example, he notes that Tutsis are slender and tall, while Hutus are short and stocky. As well, Mamdani also discusses the so-called "migration hypothesis," arguing that the Hutu and Tutsi have totally separate ancestors who both happened to migrate to the same region.
http://books.google.com/books?id=QUEamxb89JcC&pg=PA45&lpg=PA45&dq=Hutu+Tutsi+genotype&source=bl&ots=pR0794Mvlp&sig=T7nggznrQK9_cTA47hnPXbBnoow&hl=en&ei=rjT3SfGlLaPEtAPv-ejmDg&sa=X&oi=book_result&ct=result&resnum=5#PPA44,M1
According to "Lonely Planet: East Africa":
"The tall, warriorlike Tutsi people are thought to have migrated to present-day Rwanda and Burundi from Ethiopia or southern Sudan between the 14th and 17th centuries. Through their ownership of cattle and advanced combat skills, they were soon able to establish economic and political control over the local Hutu, and this dominance continues to the present day."
Many historians, anthropologists and bloggers have disputed this view, however, saying that these were attitudes that spread after East Africa was colonized, and reflected the racial views of Europeans engaging with Burundian society. (For example, there was intermarriage between Hutu and Tutsi in the pre-Colonial era, but not afterward).
http://quakerfront.com/2008/05/14/hutu-tutsi-lonely-planet/
http://quakerfront.com/2008/06/12/hutu-tutsi-before-colonialism/
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The Tutsis were slightly taller and came from Ethiopia, but the difference was more cultural than ethnic, related to social groups and types of work. After Belgium lost control of the region, the two sides were turned against each other to fuel ethnic tension, leading to the genocide.
This is the best summary of the conflict that I found, from the BBC: http://news.bbc.co.uk/1/hi/world/africa/1288230.stm
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