BACKGROUND: Macular coloboma is a rare congenital anomaly that may mimic other retinal pathologies, including infectious disease and inherited retinal dystrophies. We report a young adult male with longstanding central vision loss and bilateral macular atrophic lesions resembling coloboma, ultimately found to harbour bi-allelic pathogenic variants in ABCA4. CASE PRESENTATION: The patient underwent comprehensive ophthalmologic evaluation, including fundus imaging, optical coherence tomography (OCT), fundus autofluorescence (FAF), molecular genetic analysis, and segregation analysis. Macular dystrophy gene panel sequencing was performed. The patient was followed up for 20 years. OCT confirmed neurosensory retinal and choroidal loss at the fovea. Electro-diagnostics showed cone system dysfunction with preserved rod function. Genetic testing identified compound heterozygosity for two pathogenic ABCA4 variants (c.2160+1G>C and p.Thr1526Met), confirming ABCA4-associated retinopathy CONCLUSION: This case expands the phenotypic spectrum of ABCA4-related disease to include macular coloboma-like lesions. It also raises the possibility of coexisting retinal pathologies. Genetic testing should be considered in young patients with progressive visual loss and coloboma-like macular lesions, even in the absence of family history or evidence of intraocular inflammation. CLINICAL TRIAL NUMBER: Not applicable.