The sinoatrial node is a region of specialized cardiomyocytes that is responsible for the repetitive activity of the adult heart. The sinoatrial node is heavily innervated compared to the other regions of the heart, and the specialized cardiomyocytes of this region receive neural and hormonal input from the autonomic nervous system, which leads to changes in heart rate. A key regulator of sinoatrial beating frequency in response to autonomic input is the hyperpolarization-activated cyclic nucleotide gated (HCN) channel, a mixed cationic channel whose activity is increased by the binding of cAMP to its cytoplasmic side. HCN channels localize to distinct regions or "hot spots" on the cell surface of sinoatrial myocytes, but how these regions are formed, whether they correspond to specific signaling domains and the specific HCN isoforms and other proteins therein are not known. In this paper, we show that both HCN2 and HCN4 isoforms co-distribute with the adapter protein SAP97, an important component of distinct punctae in the sinoatrial node of the rabbit heart. HCN4, but not HCN2, also co-distributes with the post-synaptic marker beta-catenin, thus identifying diverse organized domains within this tissue. Furthermore, we show, using heterologous expression systems, whole-cell patch clamp electrophysiology and imaging, that SAP97 interacts functionally with HCN in a manner that depends upon the PDZ compatible binding motif of the C-terminus, but that its effects on I(f) behaviour are HCN isoform and context dependent. Together, the data suggest that SAP97 contributes to isoform specific organization of HCN channels within specific domains in the sinoatrial node of the rabbit.