Balancing the representation of ecosystems and threatened species habitats is critical for optimizing protected area (PA) networks and achieving the Convention on Biological Diversity strategic goals. Here we provide a systematic approach for maximizing representativeness of ecosystems and threatened species within a constrained total PA network size, using Australia as a case study. We show that protection of 24.4% of Australia is needed to achieve 17% representation for each ecosystem and all threatened species habitat targets. When the size of the PA estate is constrained, trade‐off curves between ecosystem and species targets are J‐shaped, indicating potential “win‐win” configurations. For example, optimally increasing the current PA network to 17% could protect 9% of each ecosystem and ensure that all threatened species achieve at least 78% of their targets. This method of integrating species and ecosystem targets in PA planning allows nations to maximize different PA goals under financial and geographical constraints.
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