Purpose: To study the correlation of genotype for X-linked red-green gene array with color vision phenotype in 58 subjects with red-green color vision deficiency. Methods: The molecular structure of red and green pigment genes on 58 X chromosomes was studied exon-by-exon by using heteroduplex-SSCP analysis and sequencing. The color vision of these subjects was determined by a Neitz anomaloscope. Results: Variations in the red and green pigment genes were detected in 43 subjects and a hybrid gene was found in 27 subjects. About 50% of the fusion sites occurred at intron 2-3. All 3 anomalous trichromats with intron 4 fusion were mild type but another 3 with intron 2-3 fusion were severe type. No subjects with mild type of color vision defects had a fusion site at intron 2-3 or its upstream. Three subjects with complete deletion of the green pigment gene manifested deuteranomaly. Conclusions: Protans can be differentiated from deutans on the basis of genotype. It is still difficult to establish a clear correlation of different anomalous trichromats with genotype. The fusion site of a hybrid gene affects the phenotype to some degree. Intron 2-3 is the common place for gene crossover.