The success of reductionism as a method in the natural sciences has heavily influenced modern theology, much of which attempts to reduce theology to other disciplines. However, the past few decades in science have shown the limitations of reductionism and the importance of emergence. The properties of complex systems with many constituents cannot be understood solely in terms of the constituent components and their interactions. I illustrate emergent properties and concepts with specific examples from geometry, condensed matter physics, chemistry and molecular biology. Emergence leads to a stratification of reality which affirms that ontology determines epistemology. To show the significance of emergence for the dialogue between theology and the natural sciences parallels are drawn with the theology of Karl Barth. The approach here is distinctly different from most writing on emergence and theology which embraces ‘strong’ emergence (which most scientists consider speculative), an immanent God and does not engage with orthodox Christian theology. Aspects of Barth's theology which are particularly relevant include his view that theology is an autonomous discipline which is not reducible to anthropology or history, the irreducible character of revelation, and the emphasis that ontology determines epistemology.