Collaborative innovation provides firms with a privileged opportunity to perform exploration in an externally oriented mode. The central challenges in exploration via collaborative innovation lie in the selection of relevant partners and in gaining access to potentially valuable external knowledge that the focal firm lacks. This article focuses on two aspects of inter‐organizational alignment that affect knowledge differences and may thus help explaining the shareholder value implications arising from collaborative innovation: industry and resource alignment. Relying on data covering 97 bilateral collaborative innovations (194 innovation partners) in R&D intensive high‐technology industries, we used event study methodology and follow‐up hierarchical regression analyses to test our conceptual framework. With regard to industry alignment, results suggest that investors value greater industry distance between collaborating partners, especially when the partner firm provides high‐level R&D resources. Furthermore, the results show a positive effect of supplementary resource alignment (i.e., a focal firm's R&D resources are supplemented by a partner firm's R&D resources) and, notably, a negative effect of complementary resource alignment (i.e., a focal firm's R&D resources are complemented by a partner firm's marketing resources) on investors' valuation of the collaboration's expected future performance. They, thus, contribute to research on shareholder value implications of collaborative innovation. From a managerial perspective, the study provides a better understanding of partner selection and shows how managers should position a collaboration to signal the shareholder value‐creating potential to investors.