Biological organisms use intricate networks of chemical reactions to control molecular processes and spatiotemporal organization. In turn, these living systems are embedded in self-organized structures of larger scales, for example, ecosystems. Synthetic in vitro efforts have reproduced the architectures and behaviors of simple cellular circuits. However, because all these systems share the same dynamic foundations, a generalized molecular programming strategy should also support complex collective behaviors, as seen, for example, in animal populations. We report here the bottom-up assembly of chemical systems that reproduce in vitro the specific dynamics of ecological communities. We experimentally observed unprecedented molecular behaviors, including predator-prey oscillations, competition-induced chaos, and symbiotic synchronization. These synthetic systems are tailored through a novel, compact, and versatile design strategy, leveraging the programmability of DNA interactions under the precise control of enzymatic catalysis. Such self-organizing assemblies will foster a better appreciation of the molecular origins of biological complexity and may also serve to orchestrate complex collective operations of molecular agents in technological applications.