In 1075 Alp Arslan annexed the last of the Shaddadid territories. A cadet branch of Shaddadids continued to rule in Ani and Tbilisi as vassals of the Seljuq Empire until 1175, when Malik-Shah I deposed Fadl III.

In 1085, Fadl III instigated a revolt and gained possession of Ganja. Malik-Shah launched a campaign in 1086 and removed Fadl from power again. A collateral line of Shaddadids,