In this study, we identified a family with congenital hereditary endothelial dystrophy (CHED2), which may be misdiagnosed as primary congenital glaucoma (PCG) due to similar clinical phenotypes during early infancy. A homozygous missense variant c.2024A>C, p.(Glu675Ala) in SLC4A11 was identified in the patients in this family. Our findings suggest that genome-wide neonatal screening is worthwhile to avoid the misdiagnosis of phenotypically similar diseases such as CHED2 and PCG.