Hereditary retinal disease (HRD) is a series of Mendelian diseases affecting the retina in the eye. The genetic basis of HRD is very complicated, with more than 100 disease-causing genes being identified. Though NGS has allowed rapid and large-scale mutation screening of Mendelian disease, the cost of NGS still prevents its universal application all over the world, for an accurate molecular diagnosis. Here, by clinical guidance from patient phenotypes, we performed targeted molecular diagnosis by direct Sanger sequencing of the most likely candidate gene in two families diagnosed with HRD. Then we identified two novel protein-truncating variants in the gene CRB1. Our results demonstrated the notion that molecular diagnosis and clinical diagnosis can be mutually supplemented and clinically guided direct sequencing is a cost-effective approach for molecular diagnosis and subsequent genetic counseling.