OBJECTIVE To investigate the relationship between impairment of cone/rod photoreceptors and changes in optical coherence tomography (OCT) findings. METHODS We retrospectively reviewed the clinical records of 35 patients with cone-rod dystrophy (CRD) and 35 visual acuity-matched patients with retinitis pigmentosa (RP). The presence or absence of the external limiting membrane (ELM), inner segment ellipsoid (ISe), interdigitation zone (IZ), and foveal cavitation (hyporeflective space in the outer retina) were determined using OCT image evaluation. RESULTS There were no statistical differences in the number of CRD and RP patients with an intact ELM and ISe. None of the CRD patients had an intact IZ, but 20 % of RP patients did (P = 0.011). In addition, foveal cavitation tended to be observed more frequently in CRD patients than (25.7 %) in RP patients (5.7 %) despite the difference not being significant after the correction of multiple comparison. CONCLUSIONS Eyes with CRD and RP had significant differences in foveal morphology, even when visual acuity was matched. This result supports the notion that absence of an IZ and the presence of foveal cavitation is related to cone-dominant photoreceptor impairment.