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The allo-tetraploid common carp, one widely cultured food fish, is able to produce poly-unsaturated fatty acids (PUFAs). The genetic markers on the PUFA contents for breeding was limited. The polymorphisms in <i>elovl5a</i> and <i>elovl5b</i>, the rate-limiting enzymes in the PUFA biosynthesis, have not been investigated yet. Herein, we identified one coding SNP (cSNP) in <i>elovl5a</i> associated with the content of one PUFA and two cSNPs in <i>elovl5b</i> with the contents of eight PUFAs. The heterozygous genotypes in these three loci were associated with higher contents than the homozygotes. Together with previously identified two associated cSNPs in <i>fads2b</i>, we found the joint effect of these four cSNPs in <i>fads2b</i> and <i>elovl5b</i> on the PUFA contents with the increased explained percentages of PUFA contents. The genotype combinations of more heterozygotes were associated with higher PUFA contents than the other combinations. Using ten genomic selection programs with all cSNPs in <i>fads2b</i> and <i>elovl5b</i>, we obtained the high and positive correlations between the phenotypes and the estimated breeding values of eight PUFAs. These results suggested that <i>elovl5b</i> might be the major gene corresponding to common carp PUFA contents compared with <i>elovl5a</i>. The cSNP combinations in <i>fads2b</i> and <i>elovl5b</i> and the optimal genomic selection program will be used in the future selection breeding to improve the PUFA contents of common carp.