Cardiac macrophages were recently discovered to regulate cardiomyocyte function at the atrioventricular (AV) nodes of healthy murine and human hearts. Macrophages and immune mediators have been implicated in ischemia-induced cardiac damage and arrhythmia; however, the relevance of macrophages in congenital arrhythmia pathogenesis remains unclear. Here, the wild-type (WT) mice and Calsequestrin2 gene null mutant (Casq2^-/-) transgenic model of catecholaminergic polymorphic ventricular tachycardia (CPVT) were comparatively evaluated for cardiac macrophage population at the histological level. The localization and density of the chemokine receptor, Cx3cr1-expressing cardiac macrophages were investigated ex vivo in heart sections from WT and Casq2^-/- mice at the AV node region using immunofluorescence, Masson’s Trichrome, and Hematoxylin-Eosin staining. Cx3cr1⁺ cardiac macrophages were localized in all cardiac layers and chambers of the heart, as well as septum and valve roots. Cx3cr1⁺ macrophages were coimmunostained and confirmed for expression of CD68 as a pan-macrophage marker. Macrophages were detected in close proximity to the cTnT⁺ cardiomyocytes in the myocardium of both WT and Casq2^-/- transgenic mice. Macrophage clusters were abundantly observed in the Hcn4 immunoreactive AV node region in healthy murine hearts. Subsequent quantification of signal intensities of Cx3cr1⁺ cardiac macrophages in the AV nodes in the Casq2^-/- transgenic mice was significantly lower than in WT mice. These results demonstrated a decline in Cx3cr1⁺ cardiac macrophages in AV node regions of CPVT mouse hearts, which could imply a potential contribution to arrhythmia. Our findings could serve as a valuable source for future functional investigations of macrophages in the pathogenesis of congenital arrhythmia.