This article discusses the assessment of horizontal mergers and harm to innovation when there is innovation competition. The goal is to build a scheme for the proper choice of the framework of analysis, presenting, for each situation: mechanisms to identify innovation competition, to undertake market definition, to assess the competitive significance of firms, identification of the appropriate theories of harm and evidence. We review the literature on Competition Policy and on Economics of Innovation and take examples from the US and European case law. We also briefly discuss the strategic management literature to provide insights for the assessment. Considering post-merger reductions on innovation incentives as harm to innovation, we find differences of traditional merger procedure adequacy and challenges to build evidence, considering three faces of innovation, including possible combinations of these faces within a same merger case: (i) incremental innovation efforts in the product market, (ii) ongoing efforts for developing new products and (iii) future innovation efforts. When the traditional merger procedure is inadequate, we argue in favor of using a capabilities-based assessment, changing the step-by-step procedure.