Many scholars accused that anti-Islam sentiment in many countries came after the 2001 Al-Qaeda attack. This study proves that such a phenomenon has become an issue in Indo-Pacific countries long before the attack. The article explains the root causes and impacts of Islamophobia in India, Myanmar, Thailand, and South Korea. It suggests that the regional organization should play a role in addressing this problem. The concepts of Islamophobia and national and human security are used to examine the issue. Qualitative methodology in case studies was used, with data collection from focused group discussions and literature reviews. The results show that the causes of Islamophobia range from the historical problem of colonialism, religious conflicts between majority and minority groups within a socio-political framework, separatism issues, and the medias role that stigmatizes Muslims. The Islamic-based terrorist attack in 2001 is merely a justification for violating Muslims rights in Indo-Pacific countries. This condition threatens the regions stability and leads to serious human rights violations. Therefore, ASEAN, as a regional organization in Southeast Asia and partnering with Indo-Pacific countries, must address the issue while resolving its internal challenges.