In the nineteenth century, Russian interest in the area increased greatly, sparked by nominal concern over British designs on Central Asia; by anger over the situation of Russian citizens held as slaves; and by the desire to control the trade in the region and to establish a secure source of cotton for Russia. When the United States Civil War prevented cotton delivery from Russia's primary supplier, the southern United States, Central Asian cotton assumed much greater importance for Russia.

As soon as the Russian conquest of the Caucasus was completed in the late 1850s, therefore, the Russian Ministry of War began to send military forces against the Central Asian khanates. Three major population centers of the khanates--Tashkent, Bukhoro, and Samarqand--were captured in 1865, 1867, and 1868, respectively. In 1868 the Khanate of Bukhoro signed a treaty with Russia making Bukhoro a Russian protectorate. Khiva became a Russian protectorate in 1873, and the Quqon Khanate finally was incorporated into the Russian Empire, also as a protectorate, in 1876.

By 1876 the entire territory comprising present-day Uzbekistan either had fallen under direct Russian rule or had become a protectorate of Russia. The treaties establishing the protectorates over Bukhoro and Khiva gave Russia control of the foreign relations of these states and gave Russian merchants important concessions in foreign trade; the khanates retained control of their own internal affairs. Tashkent and Quqon fell directly under a Russian governor general.

During the first few decades of Russian rule, the daily life of the Central Asians did not change greatly. The Russians substantially increased cotton production, but otherwise they interfered little with the indigenous people. Some Russian settlements were built next to the established cities of Tashkent and Samarqand, but the Russians did not mix with the indigenous populations. The era of Russian rule did produce important social and economic changes for some Uzbeks as a new middle class developed and some peasants were affected by the increased emphasis on cotton cultivation.

In the last decade of the nineteenth century, conditions began to change as new Russian railroads brought greater numbers of Russians into the area. In the 1890s, several revolts, which were put down easily, led to increased Russian vigilance in the region. The Russians increasingly intruded in the internal affairs of the khanates. The only avenue for Uzbek resistance to Russian rule became the Pan-Turkish movement, also known as Jadidism, which had arisen in the 1860s among intellectuals who sought to preserve indigenous Islamic Central Asian culture from Russian encroachment. By 1900 Jadidism had developed into the region's first major movement of political resistance. Until the Bolshevik Revolution (see Glossary) of 1917, the modern, secular ideas of Jadidism faced resistance from both the Russians and the Uzbek khans, who had differing reasons to fear the movement.

Prior to the events of 1917, Russian rule had brought some industrial development in sectors directly connected with cotton. Although railroads and cotton-ginning machinery advanced, the Central Asian textile industry was slow to develop because the cotton crop was shipped to Russia for processing. As the tsarist government expanded the cultivation of cotton dramatically, it changed the balance between cotton and food production, creating some problems in food supply--although in the prerevolutionary period Central Asia remained largely self-sufficient in food. This situation was to change during the Soviet period when the Moscow government began a ruthless drive for national self-sufficiency in cotton. This policy converted almost the entire agricultural economy of Uzbekistan to cotton production, bringing a series of consequences whose negative impact still is felt today in Uzbekistan and other republics.