Phycoerythrin (PE), phycocyanin (PC), allophycocyanin (APC), and chlorophyll a(Chl.a) are the four major photosynthetic pigments of Porphyra haitanensis. Their contents and ratio determine the blade color of Porphyra. In this study, the relative expressed levels of four pigment genes (Cpeα, Cpcα, Apcβ, and Chl.a) in different growth phases (early phase, bloom phase, and final phase) were determined using quantitative real-time PCR (qPCR) in one wild line and six pigment mutant lines of P. haitanensis. In all the lines, the relative expression levels of the four pigment genes were in the sequence: Apcβ>Cpcα> Chl.a>Cpeα. The expressed level of Cpeα varied significantly in the different phases in all the lines; however, the expressions of Cpcα, Apcβ, and Chl.a were stable in all phases in all lines. Furthermore, liner correlation and regression analysis indicated that the expression levels of the pigment genes had no relation to the pigment protein contents in any of the lines. In other words, the expression levels of the four pigment genes had no relation to the differences in blade color among the Porphyra lines. Based on these results, we speculate that the pigment mutation of P. haitanensis was induced by mutations in genes that affect the synthesis of the pigment proteins.