This article deals with the problem of the Junghar domination in the oases of Southern Xinjiang from the 1680s up to the mid-eighteenth century. It details two main aspects: (1) the policy and administration of the Junghars in Xinjiang; (2) the struggle of the Uighur people [sic] against this domination. After recalling the strong presence of the Naqshbandi Khwajas in the political and legal system of the Yarkand Khanate, then the alliance between one branch of them (Afaq Khwaja and the Afaqis/Aqtaghliqs) and the Jungars which led to the fall of the Khanate, the author analyzes the Junghar rule: the application of the barimtayliq rule, i.e. the forced exile of local elites to Ili; the tax collect on agricultural and pastoral products (with several facts and figures); the introduction of a new currency. Beyond the usual Marxist-Maoist thesis (the people’s struggle against feudalism), this study shows through major events how these iniquitous rules caused discontent and opposition among the society.