After Tashkent’s fall General M. G. Chernyaev became the first governor of the new province of Turkestan, and immediately began lobbying to keep the city under Russian rule and to embark on further conquests. An apparent threat from Sayyid Muzaffar, Amir of Bukhara, provided him with a justification for further military action, but he retreated before the fortified town of Jizzakh and was recalled shortly afterwards. His successor, General D. I. Romanovskii, defeated the Bukharan forces at the Battle of Irjar, and then launched unauthorised assaults on Khujand and Jizzakh, adding further to Russian territory. After a brief lull, during which Turkestan was made a Governor-Generalship under General K. P. von Kaufman, war with Bukhara broke out again in 1868. Von Kaufman’s forces defeated Amir Sayyid Muzaffar’s army at Chupan-Ata, outside Samarkand, and at the Zirabulak heights. After the Russian garrison in the Samarkand fortress had been besieged and relieved, the whole of the upper Zarafshan valley was annexed to Russia and the Bukharan Emirate’s remaining territory became a Russian protectorate. Von Kaufman realised that in order to have a stable relationship with Bukhara he would need to strengthen the Amir’s authority, which he did by crushing the independent city-state of Shahrisabz and handing it over to Bukharan rule.

The final phase of Russian expansion in Central Asia occurred in some of the most remote and inhospitable territory on the planet – the high Pamir plateau and the valleys of Shughnan, Roshan and Wakhan, inhabited by sparse populations of Kyrgyz and Pamiri Tajiks. The latter were considered by the Russians to be the last remnants of the autochthonous ‘Aryan’ population of Central Asia, and became an object of ethnographic fascination for this and their Isma’ili religion. Faced with the threat of domination by Sunni Muslim lowlanders – whether in Afghanistan or Bukhara – for many Pamiris Russian rule was a more attractive option. This was perhaps the one phase of the conquest where the old Soviet trope of ‘voluntary uniting’ contains a grain of truth – the Pamiris actively lobbied for a Russian presence on their territory, and proved adept at manipulating it to their advantage. The Pamirs were also the site of some of the most mythologised episodes of the ‘Great Game’, but, while the British were concerned by Russian activities, in 1895 they came to an amicable agreement on the drawing of a new frontier along the river Panj. The problems with Bukharan rule over Shughnan, Roshan and Wakhan proved much more intractable, and led to the imposition of direct Russian rule in 1905.