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The Galapagos Islands, a UNESCO World Heritage Site renowned for their unique biodiversity, face escalating ecological threats from unsustainable tourism-driven development. Protected habitats and conservation policies have preserved much of the archipelago’s ecological function, but growing tourism and urban settlement—concentrated on a narrow ~ 3% of inhabitable land—have strained ecosystems and disrupted wildlife cycles. These dynamics reveal the limits of a “natural laboratory” framing and demand a shift from a binary human versus nature model to a sustainable human-with-nature approach. Reconciling local livelihoods and biodiversity therefore requires integrated, site-specific strategies that treat the built environment as an active component of conservation. This study proposes an architectural response exploring how human-centered spaces can coexist with habitats for other species while avoiding further degradation of ecological integrity, ultimately enhancing resilience. Using a research center modeled after the Charles Darwin Foundation on Santa Cruz Island as a design case, the proposal integrates animal-aided design (AAD) and climate-responsive principles. Central to the investigation is enabling humans to inhabit spaces alongside other species while respecting ecological cycles, safeguarding the Galapagos’ natural heritage, and supporting sustainable development. Programmatically, roughly half the total area is allocated to species-specific zones, reflecting a deliberate balance between conservation and research/education. Site selection balances proximity to settlements, minimizing transport-related disturbance, with isolation to foster wildlife habitation. Five keystone species—land and marine iguanas, giant tortoises, sea lions, and Darwin’s finches—guide ecosystem-sensitive strategies for shared habitats. Design innovations include elevated platforms preserving animal movement, open-flow layouts responsive to equatorial climate, multi-layered structures minimizing land footprint, and natural recyclable materials supporting passive climate control. Building forms adapt to topography, avoiding visual dominance and fostering ecological integration. Through this sequenced design process, the outcome of this novel AAD + climate-responsive design integration demonstrates architecture’s potential to harmonize human and non-human occupancy, preserving ecosystems while supporting scientific and educational functions.