The centers of trade and economic activities in the region of Southeast Asia rank from a huge and modern to a small and traditional pattern. Malacca and Singapore have been cases in point for huge and modern patterns, while the border areas in eastern Indonesia, East Malaysia, and the Philippines are the cases for small and traditional centers. This paper will argue that with global connectivity and regional dynamics, the small and traditional trade and economic centers could shift to modern ones. History records that the introduction of the Southeast Asian region by the outside world, especially in relation to trade and economic activities, was largely derived from the significant role played by the people in the mainland of Southeast Asia regarding the silk roads route and the role of the people in the insular or islands of Southeast Asia regarding the spice trade route in the premodern time. Later in the modern time in Southeast Asia, the role of Islam, the Europeans and the center trade of Malacca around the 17th and 18th centuries played a significant role. Indeed, huge trade centers like Malacca in the 17th C and 18th C and later by Singapore in the 9th C have been very important throughout the history of trade in the Southeast Asian region. However, we must not ignore the roles of the border areas in the Southeast Asian archipelago, especially in eastern Indonesia, East Malaysia, and the border region of the Philippines which have played a dominant role in trade and economic activities. These activities have been smaller and more traditional than the Malacca and Singapore cases, but economic activities could develop rapidly with the global connection and its interconnectivity. Besides, those border areas have also become an important key for security issues not only in the Southeast Asia region in particular but also in the Asia Pacific or Indo Pacific region as well. The security of the region of Southeast Asia and even Indo Pacific could be affected by the situation in those border areas. Interconnectivity is a challenge as well as an opportunity for these border areas to become the future of trade and economic activities within the region of Southeast Asia that also connects with the region of Indo Pacific, especially China, South Korea, and Taiwan. The planning of Indonesian capital movement to East Kalimantan will add opportunities for those border areas located near the proposed new capital. About the above issues, this paper will address several issues: firstly, the history of trade and economic activities in Malacca, Singapore, and the border areas in eastern Indonesia, East Malaysia, and the Philippines; secondly, the different patterns of trade and economic developments of the Malacca, Singapore, and the border areas in eastern Indonesia, East Malaysia, and Philippines; thirdly, the challenges and opportunities of the border areas in eastern Indonesia, East Malaysia, and the Philippines to develop bigger trade centers in the future; fourth, the interconnectivity of those border areas to Asia Pacific region. This paper uses an interdisciplinary approach in the fields of social sciences and humanities. With this study, it is hoped that a better understanding of regional dynamics will be obtained, especially in the border areas. The period that we use is from 1998 until present time regarding if there was changing policy due to the end of Old Order to the Reformation period of Indonesian government. As a result, the development of border areas had been in existence before the colonial time in which people moved freely and had trade contacts. Even though they used to have the same ethnic linkage, after the formation of a modern state where they have different citizenships, in reality they can relate to each other in harmony and peace because of the similarity of ethnic linkages they had in the past. Colonial powers intended to replace the powers of traditional kingdoms with the idea of civilizing the colonializ