Khoja or Khwaja, a Persian word literally meaning 'master', was used in Central Asia as a title of the descendants of the noted Central Asian NaqshbandiSufi teacher, Ahmad Kasani or others in the Naqshbandi intellectual lineage prior to Baha al-din Naqshband. The most powerful religious figure in the late Timurid era was the Naqshbandi ShaykhKhwaja Ahrar. The Khojas often were appointed as administrators by Mongol rulers in the Altishahr or present-day region of Tarim Basin in Xinjiang, China. The Khojas of Altishahr claimed to be Sayyids and they are still regarded as such by the fraternity people of Altishahr. Although Ahmad Kasani himself, known as Makhdūm-i-Azam or "Great Master" to his followers, never visited Altishahr, many of his descendants, known as Makhdūmzādas and bearing the title Khoja played important parts in the region's politics from the 17th to 19th centuries. On the death of Aḥmad Kāsānī, a division took place among the Khojas which resulted in one party becoming followers of the Makhdum's elder son Khoja Muhammad Amin better known as Ishan-i-Kalan and another attaching themselves to his younger son Khoja Muhammad Ishaq Wali. The followers of Ishan-i-Kalan seem to have acquired the name of Aq Taghliqs or White mountaineers and that of Ishaq Qara Taghliqs or Black mountaineers but these names had no reference to the localities where their adherents lived. All were inhabitants of the lowlands and cities of Eastern Turkistan but each section made allies among the Kyrgyz of the neighboring mountains and apparently subsidized them in their internecine battles. The Kyrgyz tribes of the Western Tian Shan ranges lying to the north of Kashghar were known as the White mountaineers and the Kyrgyz tribes of the Pamir, Karakoram and Kunlun as the Black mountaineers with Yarkand as their main city of influence, such that the Khojas came to assume the designations of their Kyrgyz allies. The Turki languageTadhkirah i Khwajagan was written by M. Sadiq Kashghari.
Note: The following list is incomplete and, at times, possibly slightly inaccurate. It also excludes several collateral lines that ruled over minor territories and were relatively unimportant.
Blue row signifies progenitor of the Khojas of Altishahr.
Azim Malikov, Kinship systems of Xoja groups in Southern Kazakhstan in Anthropology of the Middle East, Volume 12, Issue 2, Winter 2017, pр.78-91
Azim Malikov, Sacred Lineages in Central Asia: Translocality and Identity in Mobilities, Boundaries, and Travelling Ideas: Rethinking Translocality Beyond Central Asia and the Caucasus edited by Manja Stephan-¬Emmrich and Philipp Schröder, 2018, pp.121-150
Azim Malikov, Khoja in Kazakhstan: identity transformations in Max Planck Institute for Social Anthropology Department ‘Integration and Conflict’ Field Notes and research Projects VI CASCA – Centre for Anthropological Studies on Central Asia: Framing the Research, Initial Projects. Eds.: Günther Schlee. Halle/Saale, 2013, pp.101-107