Abstract Background: The purpose of this study is to determine the genetic association and compare the distribution of ABCA4 gene variants in patients with various inherited retinal dystrophies, including autosomal recessive cone-rod dystrophy (AR-CRD) autosomal recessive retinitis pigmentosa (AR-RP) in the South Indian cohorts. Methods: This study included nineteen probands, ophthalmic examination of all the probands were carefully evaluated by the Paediatric Ophthalmologist. Eleven of the nineteen probands had the clinical phenotype of AR-CRD, eight showed AR-RP-like clinical phenotype. Genomic DNA was extracted from their peripheral blood, the exon and intronic boundaries of the ABCA4 gene were screened using the Sanger sequencing to identify the genetic association of these two retinal dystrophies. Results: Sanger sequencing results revealed that only 18% (2/11) of AR-CRD probands had disease-causing ABCA4 mutations, while the remaining 9 AR-CRD, 8 AR-RP were negative for the pathogenic variant associated with ABCA4. Furthermore, this study identified 18 common SNPs of the ABCA4 (2 missense, 3 synonymous, 13 intronic variants) and found them associated with AR-CRD and AR-RP probands. Conclusion:This is the first study to show that two missense variants in the ABCA4 (c.302T > C, c.1319A > G) are associated with AR-CRD probands and two rare NNCS variants (c.3191-10G > T, c.3814-5G > A) associated with AR-RP patients from the South Indian population.