The color of pearl, one of the important quality traits, is determined by the shell nacre color of host mussel; however, the effective method to evaluate the effect of genetic breeding on the purity and uniformity of the nacre color was still limited to the freshwater mussel Hyriopsis cumingii. In this study, the characteristics of the υ₁ band of polyene pigments in the colorful shell nacre and pearl samples from different selective generations of H. cumingii were detected by Raman spectroscopy. The results of this study showed that the number of peaks at the υ₁ band of polyene pigments decreased gradually from 6–8 in the shell nacre and pearls with the color scheme of purple for wild mussels to 1 in those from the mussels of the F4 generation by genetic breeding. Similar results were also found in the samples with the color scheme of orange. But, no obvious peak of the υ₁ band was detected in the samples with white color after four generations of selective breeding. Thus, it could be speculated that the single peak of the υ₁ band in the Raman spectroscopy of shell nacre could be used as the sign of color uniformity to reflect the degree of purification in shell nacre color by genetic breeding. Meanwhile, the results showed that the samples with the same color scheme have a similar main peak at the υ₁ band (ca. 1,508 cm^–1 for the purple color scheme and ca. 1,528 cm^–1 for the orange color scheme), suggesting that the polyene pigments in shell nacre and pearl with the same color scheme have the same length of C = C double bond. The length of C = C double bond were 12 and 9 in purple and orange samples, respectively. In summary, the results of this study support the conclusion that Raman spectroscopy is an efficient method to evaluate the genetic breeding for nacre color in H. cumingii.