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<b>AIM:</b>To identify the genetic defects in a Chinese family with achromatopsia.<b>METHODS:</b>A 2.5-year-old boy, who displayed nystagmus, photophobia, and hyperopia since early infancy, was clinically evaluated. To further confirm and localize the causative mutations in this family, targeted region capture and next-generation sequencing of candidate genes, such as <i>CNGA3</i>, <i>CNGB3</i>, <i>GNAT2</i>, <i>PDE6C</i>, and <i>PDE6H</i> were performed using a custom-made capture array.<b>RESULTS:</b>Slit-lamp examination showed no specific findings in the anterior segments. The optic discs and maculae were normal on fundoscopy. The unaffected family members reported no ocular complaints. Clinical signs and symptoms were consistent with a clinical impression of autosomal recessive achromatopsia. The results of sequence analysis revealed two novel missense mutations in <i>CNGA3</i>, c.633T&gt;A (p.D211E) and c.1006G&gt;T (p.V336F), with an autosomal recessive mode of inheritance.<b>CONCLUSION:</b> Genetic analysis of a Chinese family confirmed the clinical diagnosis of achromatopsia. Two novel mutations were identified in <i>CNGA3</i>, which extended the mutation spectrum of this disorder.