QaraQoyunlu and AqQoyunlu governments encountered several political and military crises in their reigns; among the effective factors tribal structure of the confederationwas of special importance. The role of tribal structure in political instability of Turkmen governments will be explained in this article with free use of conflict theory، and causal analysis، and comparing method. Hypothesis stands for tribal structure، making conflicts in variety of aspects، increased tribal tendency in army، wing tendencies in tribes، and pole tendencies inconfederation. This، by making conflicts in 3 levels (conflict between tribes and government، intraconfederation conflict، and intratribal conflict) prevented tribes from gathering with new aspects of centralized power; and lead to tendency to princely rebellions. As a result، governments have been destroyed by external forces at their highest point of power.