This article is intended to comment on the civilisational history of Islam in Southeast Asia. The history is explained and accounted for in terms of the three major waves of globalisation that have impacted the region since the arrival of Islam as early as the eleventh century. The first wave, itself initiated and dominated by Islam, was responsible for the introduction and establishment of Islam in the region to the point of becoming its most dominant civilisation. The expansion of Islam and its civilisation was in progress when the second wave hit the shores of the Malay-Indonesian Archipelago with the arrival of the Portuguese and other Western powers resulting in the colonisation of the region. The third wave, an American-dominated one, manifests itself in the post-colonial period which witnesses Southeast Asian Islam reasserting itself in various domains of public life. The author sees Southeast Asian Islam as the historical product of centuries-long civilisational encounters with the pre-Islamic indigenous cultures and civilisations and later between ‘Malay-Indonesian Islam’ and the newly arriving religions and cultures brought by both the colonial and post-colonial West, arguing that Islam in the region has been significantly impacted by each of the three waves.