The Merkits lived in the basins of the Selenga and lower Orkhon River (modern south Buryatia and Selenge Province).

[citation needed] The Merkits were a confederation of three tribes, inhabiting the basin of the Selenga and Orkhon Rivers.

In turn, Temüjin's new wife Börte was kidnapped by Merkit raiders from their campsite by the Onon river around 1181 and given to one of their warriors.

Temüjin, supported by his brother (not blood-related) Jamukha and his khan etseg ('khan father') Toghrul of the Keraites, attacked the Merkit and rescued Börte within the year.

By the time he had united the other Mongol tribes and received the title Genghis Khan in 1206, the Merkits seem to have disappeared as an ethnic group.

In 1236, during the Mongol invasion of Volga Bulgaria, a body of the Merkit was found in the area of land dominated by the Bulgar and Kipchak.