Indonesia is a nation of diversity. Thus various traditions, cultures, religions, beliefs, ethnics, tribes and languages were united when the Republic was founded. Based on those facts, Indonesia’s founding fathers showed strong efforts in uniting the existing diversity and political currents under the national concensus ‘Bhinneka Tunggal Ika’, Hindu-Sankrit words meaning unity in diversity, and The Pancasila, five national basic principles. Consequently national law, mechanism of governance and political considerations followed the concept of Indonesia as a secular nation-state. It means that Indonesia also respects to the international law, human rights, and democracy, such as freedom of association and press, as well as the idea of individual human rights. From a perspective of human rights, the legitimacy of self determination for each human includes the aspect of sexual orientation and living in partnerships. Factually, people who perform their ‘coming out’ and those who advocate understanding or empathy on lesbian, gay, bisexual and transgender (LGBT) issues, so far experience little support, yet often harsh negative reactions, pressure, and harassment particularly from traditionalistic and religious communities that see a diversification of forms of partnership and sexual orientation as un-Indonesian or sinful. This article will show the emerging of LGBT movement, and human security concept relating to the government policies. Moreover, it tries to describe the second wave of modernization leads to a reinterpretation of traditional reference frames such as religion, particularly in Islamic context, and to approach that aim to bridge the gap between changing social reality and religious teaching.