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The ethnic conflict, the Tamil’s separatist struggle and the counter state violence in Sri Lankan context have come to affect the conditions of normalcy not only in the Northern Province but also in the Eastern Province. Amidst this ethnic conflict and its causes in Sri Lanka, the Muslim community in the Eastern Province was also severely affected. In addition to the Northern Muslims, the Eastern Muslims have come to face number of grievances caused by both parties in the conflict: killings, abductions, displacements and loss of properties and livelihood are some of the aspects to be mentioned. The Muslims in both Provinces did not extend their support either in the battlefield or in the separatist movement. Besides, their grievances were not given due consideration and reconciled by the respective authorities in the government and by the parties in the ethnic conflict resolution process. These grievances and the constant negligence of the interests of the Eastern Province Muslims have come to force them to raise the demand for the territorial autonomy for them in the region. It is similar to Tamils’ demand, to safeguard their rights and recognize their existence as an entity, to accept their distinct religious identity and to ensure their self-determination.