Objectives: To examine the partnerships in population health planning between Medicare Locals (MLs) and Local Health Networks (LHNs) in South Australia, and the factors that facilitated or constrained collaborations, to offer lessons for LHNs and Primary Health Networks. Design, participants and setting: We conducted a qualitative study using individual interviews with key informants (executive or program leader staff) from the five South Australian MLs and the five South Australian LHNs. A total of 34 interviews were conducted between March and July 2014. Results: Significant work was undertaken by MLs in the process of population health planning and needs assessment. Participants from both MLs and LHNs described examples of collaborative work, including data sharing and synthesis, program implementation and community consultation. The focus of LHNs on acute and intermediate care, the lack of system-level strategies to support collaboration, and constant policy and structural changes leading to uncertainty in the primary health care landscape were perceived as key barriers to collaboration. Conclusions: The experience of MLs and their achievements in building relationships and trust with stakeholders in their regions, including LHNs, provide valuable lessons for the new Primary Health Networks in Australia.