This paper represents the root causes of Hazaras persecution in Afghanistan through ethno-religious and psycho-cultural approaches, using Protracted Social Conflicts (PSC) and Relative Deprivation (RD) frameworks. The Hazara community has been subject to persecution in variety of ways including assassinations, physical torture, enslavement, forced displacement, kidnapping, and target attacks by both state and non-state actors. This study explored multifrontal causes consisting international connection, structural inequalities, communal cleavages, access to economy and power, and interpersonal and ingroup values contributed to Hazaras persecution in Afghanistan. This study argues that the excessive persecution and discrimination against Hazara community was founded, particularly by Abdul Rahman in 1890s which shaped the ethno-religious and psycho-cultural approaches of Hazaras afterward. The ethno-religious and psycho-cultural approaches led the common thinking against Hazaras in the form of wrong identification, wrong myths, false consciousness, and ill-definition of Hazaras as monolithic Shi’as who have consistently been labelled as “Kafirs,” unbeliever, and decedents of Genghis Khan. The persecution of Hazaras can be studied through the lens of PSC, manifests the longstanding inter-state and intra-state conflicts, and RD depicts comparison of disadvantagedness of an individual or a group with other individuals and groups.