Ayombekov had been a warlord during the 1992 to 1997 Tajik Civil War between the United Tajik Opposition and the government led by President Rahmon Nabiyev.
Following the treaty, several units of the Opposition became part of the Tajik National Army, becoming some of its most experienced units.
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During the Tajikistan Civil War from 1992–1997 Pamiris in large backed the United Tajik Opposition, the Pamiris were targeted for massacres, especially those living in the capital Dushanbe and Qurghonteppa Oblast.