In the final years of the Soviet Union , the region again became a source of dispute between Armenia and Azerbaijan , culminating in the Nagorno-Karabakh War of 1988-1994 . In the final years of the Soviet Union , the region re-emerged as a source of dispute between Armenia and Azerbaijan , culminating in a large ethnic conflict and , eventually , in the Nagorno-Karabakh War that was fought from 1991 to 1994 .