Conceptualizations of modern Indonesia were active agents in shaping the way we saw the present Indonesia and its problems. This study is concerned with some major conceptions of modern Indonesia, namely, the primordial sentiments thesis, the transitional stage thesis, the historical structural thesis, and the cultural imperialism thesis. Our specific interest was on comparing the way they treated the Indonesian state and society. It is our argument that involvement of scientific knowledge in the formation of modern Indonesia had been a complex process: scientific knowledge intertwined with common sense in power relations. This had meant Indonesian societies and identities could never be considered to have been monolithic.