This study investigates the problem of ecosystem dynamics in fragmented landscapes, specifically focusing on a two-patch environment with interacting prey and predators. The research examines the impact of cross-predation on these interactions. Using bifurcation analysis, we explored the structural arrangement of attractors and identified complex dynamics such as symmetric, asymmetric, and asynchronous attractors induced by varying cross-coupling levels. Notably, our study describes a novel mechanism for the formation of anti-phase synchrony in the patches. Unlike typical occurrences of a cycle following Hopf bifurcation, our model reveals that the anti-phase cycle stabilizes via Neimark-Sacker (NS) bifurcation of a two-period unstable cycle branch emanating from the synchronous cycle branch. Our findings also demonstrate that cross-feeding can lead to significant ecosystem asymmetry and branching, culminating in the dominance of a single cross-feeding chain. These results challenge traditional models and highlight the presence of multistability and the potential for ecosystem evolution towards distinct subsystem branches due to cross-predation. The study’s insights offer valuable contributions to population and evolutionary biology, enhancing our understanding of the intricate dynamics within fragmented ecosystems. This study investigates the problem of ecosystem dynamics in fragmented landscapes, specifically focusing on a two-patch environment with interacting prey and predators. The research examines the impact of cross-predation on these interactions. Using bifurcation analysis, we explored the structural arrangement of attractors and identified complex dynamics such as symmetric, asymmetric, and asynchronous attractors induced by varying cross-coupling levels. Notably, our study describes a novel mechanism for the formation of anti-phase synchrony in the patches. Unlike typical occurrences of a cycle following Hopf bifurcation, our model reveals that the anti-phase cycle stabilizes via Neimark-Sacker (NS) bifurcation of a two-period unstable cycle branch emanating from the synchronous cycle branch. Our findings also demonstrate that cross-feeding can lead to significant ecosystem asymmetry and branching, culminating in the dominance of a single cross-feeding chain. These results challenge traditional models and highlight the presence of multistability and the potential for ecosystem evolution towards distinct subsystem branches due to cross-predation. The study’s insights offer valuable contributions to population and evolutionary biology, enhancing our understanding of the intricate dynamics within fragmented ecosystems.