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Background Blue and green light fundus autofluorescence (FAF) imaging methods are used routinely in inherited retinal disease assessment. Here, we explored the central foveal appearance with these modalities in patients with CNGB3-associated achromatopsia, as well as central foveal ellipsoid zone (EZ) continuity on optical coherence tomography.Methods Forty-one patients (24 females; mean (SD) age, 32 (19) years) imaged with both blue-light FAF (488nm, Heidelberg Spectralis) and green-light FAF (532nm, Optos plc), from a tertiary eye hospital, were retrospectively reviewed. The fovea was graded qualitatively as hypo- or hyper-autofluorescent relative to the parafovea. Spectral-domain optical coherence tomography (OCT) from the same visit, graded independently and masked to FAF grading, was also assessed for continuity of the foveal ellipsoid zone (EZ).Results The central fovea appeared hypoautofluorescent on blue FAF in all cases. However, 11 patients (27%) showed a relatively hyperautofluorescent central fovea on green FAF, indicating discordance between modalities. Discordant patients were significantly younger than concordant patients (p = 0.022). The EZ was gradable in 40 patients, 22 of whom displayed a continuous EZ in both eyes. These individuals were significantly younger than those with EZ interruption (p < 0.0001). All patients with discordant FAF findings had a continuous foveal EZ.Conclusions More than one quarter of our cohort of CNGB3-achromatopsia patients demonstrated central foveal signals that were discordant between blue and green FAF; all had a continuous EZ. This suggests that the two platforms are not interchangeable and investigating discordance could yield insight into disease mechanisms.