Highly unsaturated fatty acids (HUFAs) are crucial for the nutritional health, physiology, and reproduction of vertebrates. The Δ6-desaturase and Elovl5 elongase genes produce essential enzymes in the biosynthetic pathway of HUFAs. Single nucleotide polymorphism (SNP) analysis of genes functionally related to the growth traits of the common carp (Cyprinus carpio var. Jian) can provide useful information for common carp molecular breeding. In this study, we isolated two Δ6 Fad genes and two Elovl5 genes from the common carp.