Among the Mongol leaders, the strongest in the Central Asian region was Timur and his descendants, who came to power in the mid- to late-1300s and ruled until the 1500s. These people ruled the region with few challenges and fully developed the Silk Trade Route as well as major cities along the path, most of which are in modern day Uzbekistan, including their capital of Samarkand.
After the fall of the Timurid Dynasty few strong leaders ruled over the Tajik people, or Central Asia as a whole, until 1868 when the Russians took the region. The Russians moved into the region for numerous economic reasons, and with no organized government and few arms to fight, the region of Central Asia, including what is today Tajikistan soon fell under Russian control.
The Tajiks remained under Russian rule until Russia fell and was replaced by the Soviet Union. The Tajiks immediately fell under Soviet control as borders were shifted in order to create ethnic diversity in the region, and hence a smaller chance of an uprising against the Soviet government. This led to the removal of Bukhara and Samarkand from Tajik control to Uzbek control as the government encouraged Tajiks to view themselves as Uzbeks.
Under Soviet rule Tajikistan, like many of its neighbors, suffered greatly. First with the loss of their two major cities, but that continued as the region soon became the poorest part of the entire Soviet Union. Due to the nearly inaccessible mountains and strong Islamic influence in the south the people of Tajikistan never truly succumbed to Soviet demands, which is part of the reason they suffered so greatly.