Archaeological indications suggest that the first human inhabitants of the Pamirs derived from two massive waves of migration of Aryan tribes from the plains of Asia; one moved southwards towards India and the other turned towards Persia and then gradually towards Europe.  Thus the Indo-European race is said to have spread to two continents of the world.  

By the second and third century AD, there were small kingdoms in the Wakhan and Shugnan.  These kingdoms later became part of the Akhemenid Persian Empire.  Subsequently, this empire was conquered by Alexander the Great, after which the area came under the rule of the Khushanids from Northern India and the Sasanids from Persia.  These semi-independent statelets continued to exist through to the early 20th century.  

When the Sasanids were defeated at the start of the 8th century, Islam began to spread in the area to supplant Zoroastranism and Buddhism, the latter being widely practiced in the Wakhan at that time.  In the 13th  century, the explorer Marco Polo wrote that the process of conversion to Islam was almost total.  

During the middle ages, the Pamirs were ruled by various dynasties including the Samanids, the Ghaznavids, the Mongols, the Temurids, the Shaibanids and the Safavids, all for relatively short periods of time. None of these foreign rules lasted permanently. At times,  the Wakhan and Shugnan experienced onslaughts of marauding raids by Turkic and Mongolian invaders, from the western territories under the nominal rule of the Chinese Empire.  Despite its geographical isolation and relative independence from the outside world, Badakhshan had close links with other regions in Central Asia. Throughout the pre-modern era, it maintained economic and cultural ties with Bukhara, Khujand, Qoshghar and, most importantly, with the Ismaili communities in northern India and western China.  

Towards the beginning of the 19th century, Tzarist Russia sought political interests in Central  and South Asia. As the main political rival of the  British  rule in India, Russia  tried to establish a presence in the region. As a consequence, the territories under present Tajik and Afghan Badakhshan became the arena of intense geopolitical confrontation between these two powers which were vying for control over the area linking Europe and Asia.  These disputes over this specific territory, during this time period are historically labelled as ‘The Great Game’.

As of  1872 – 1873,  Tzarist Russia and British India negotiated on the division of the disputed territories .  While the British insisted on the sovereignty of Afghanistan, the Russians pressed for the jurisdiction of Bukhara, their protectorate in Central Asia. 

In 1895 an agreement was signed between Tzarist Russia and Great Britain that established borders, which divided the Western and the Eastern Pamirs.  This resulted in the Western Pamirs coming under the rule of the Emir of Bukhara whereas the Eastern Pamirs, along with the upper Bartang valley, came under direct Russian protection. 

Following this agreement,  the Russian White Army established its garrisons in Khorog and Murghab and the Pamirs officially came under  Russian protection.    During this transition period,  Bukhara still had some influence on the area through tax-collection and intimidation but eventually these practices were brought to a halt by the Russian military authorities.   The authorities then began setting up structures of civil administration in Gorno-Badakhshan,  ended the local turf wars,  as well as  the then common slave trade in the Pamirs.  This rule continued   when the Communists assumed power in Russia in 1917.  

Between the 1930s  and 1940s, the population of the Pamirs suffered under Stalinist repression.   Community and religious leaders and intelligentsia  were either executed or exiled to Siberia.  During the Second World War, however, through necessity, Stalin had to show a benign face and managed to conscript many young Pamiris to the Soviet Army to fight the so-called Great Patriotic War.   

After the Second World War, the Pamirs benefitted from Soviet subsidies and were able to make strides in education and economic development.   In the early 1990s, Badakhshani intelligentsia  were actively engaged in the process of perestroika and glasnost, demanding social justice and equal distribution of resources.  Post Soviet-Russia, a civil war broke out in Tajikistan; Badakshanis wanted autonomy but this goal was never realized, since it was  never supported by either the Central Authorities in Dushanbe nor by the establishment in Moscow.  

At the end of the Civil War in 1997, Gorno Badakhshan was recognized as an inseparable part of the unitary state of Tajikistan although it continues to hold the status of ‘autonomous region’.