Why and when does party headquarters grant autonomy to its local branches, and what trade-offs ensue when providing such discretion? This article tackles these broader questions by focusing on a largely under-investigated area: the impact of directly elected governors and mayors on intra-party dynamics. To facilitate analysis, the article borrows from the ‘delegation’ and ‘franchise’ models, which seek to explain how party organizations adapt to multi-level electoral environments. Sources of intra-party conflict over gubernatorial campaigns derive from theories of party behaviour under presidential systems. Empirical evidence is provided by examining how Japan’s two major parties have dealt with gubernatorial campaigns in recent years. Select cases and data demonstrate how local units are driven by differing incentives from the national leadership, the consequent intra-party conflicts and the limited success of party headquarters in steering its local units. The article discusses the extent to which the ‘franchise’ or ‘delegation’ models successfully capture the way in which the two Japanese parties have engaged in gubernatorial campaigns. To illustrate generalizability beyond Japan, the article ends with a brief comparative counterpoint: intra-party conflict over the selection of the Greater London Authority’s mayoral candidate in 2000 and 2004.