PurposeFoveal center marking is a key step in retinal image analysis. We investigated the discordance between the adaptive optics (AO) montage center (AMC) and the foveal pit center (FPC) and its implications for cone mosaic analysis using a commercial flood-illumination AO camera.MethodsThirty eyes of 30 individuals (including 15 healthy and 15 patients with rod–cone dystrophy) were included. Spectral-domain optical coherence tomography was used to determine the FPC, and flood-illumination AO imaging was performed with overlapping image frames to create an AO montage. The AMC was determined by averaging the (0,0) coordinates in the four paracentral overlapping AO image frames. Cone mosaic measurements at various retinal eccentricities were compared between corresponding retinal loci relative to the AMC or FPC.ResultsAMCs were located temporally to the FPCs in 14 of 15 eyes in both groups. The average AMC–FPC discordance was 0.85° among healthy controls and 0.33° among patients with rod-cone dystrophy (P < 0.05). The distance of the AMC from the FPC was a significant determinant of the cone density (β estimate = 218 cells/deg2/deg; 95% confidence interval [CI], 107–330; P < 0.001) and inter-cone distance (β estimate = 0.28 arcmin/deg; 95% CI, 0.15–0.40; P < 0.001), after adjustment for age, sex, axial length, spherical equivalent, eccentricity, and disease status.ConclusionsThere is a marked mismatch between the AMC and FPC in healthy eyes that may be modified by disease process such as rod–cone dystrophy. We recommend users of AO imaging systems carefully align the AO montage with a foveal anatomical landmark, such as the FPC, to ensure precise and reproducible localization of the eccentricities and regions of interest for cone mosaic analysis.