Although REDD+ was conceived as a national approach to reducing emissions from deforestation and forest degradation, many of the early advances have been at the subnational level. It is critical to link these subnational efforts to emerging national REDD+ frameworks, including with respect to finance and benefit distribution, setting reference levels, measurement, reporting and verification (MRV), land policy and safeguards. We use evidence from interviews with proponents from 23 subnational REDD+ initiatives in six countries to characterize the multilevel governance challenges for REDD+. We analyse the differences in perceived challenges between subnational jurisdictional programs and project-based initiatives, and then analyse proponents' perceptions of the relationship between government policies at multiple levels and these REDD+ initiatives. We find important multilevel governance challenges related to vertical coordination and information sharing and horizontal and inter-sectoral tensions, as well as concerns over accountability, equity and justice. Though the shift to a nested, jurisdictional or national REDD+ is sometimes approached as a technical design issue, this must be accompanied by an understanding of the interests and power relations among actors at different levels. We outline challenges and suggest priority areas for future research and policy, as countries move towards a national REDD+ system.