The architecture of innovation ecosystems—the distribution of productive activities and the structure of exchanges that integrate outputs—varies widely, and it has major implications for how ecosystems create value and which participants capture value. Some ecosystems are built around central platforms or standards, while others are not, and among platform-based ecosystems, the extent to which platform governance is centralized versus decentralized varies extensively. Existing strategy research lacks an account of which ecosystem architectures fit which contextual conditions, tending instead to attribute architecture to firms’ strategies and capabilities. In this paper, I analyze key dimensions of variety in ecosystem architectures to generate a typology of three ideal-type ecosystem architectures: firm-controlled platforms, shared-governance platforms, and symmetric-populations ecosystems. Building on this typology, I propose a discriminating alignment theory that explains why certain architectures fit specific configurations of contextual conditions. The discriminating alignment framework draws on foundations from transaction cost economics, modularity, and the game-theoretic approach to technical coordination. The framework maps the three ecosystem architectures, as well as a vertically integrated baseline architecture, to contextual conditions of value proposition complexity, demand heterogeneity, and environmental dynamism. The paper contributes to strategy research by helping us understand the antecedents of ecosystem architecture and by situating platforms and ecosystems within the markets-and-hierarchies framework of institutional economics.