As the most intuitive phenotype, the length of the maxilla of Coilia nasus has always been considered as the main feature that distinguishes different ecological groups of C. nasus. Endothelin 1 (Edn1) plays an essential role in jaw development. Based on the previous genome re-sequencing results and the C. nasus genome database, the Edn1 gene sequence was isolated using PCR amplification to investigate the effect of Edn1 gene on the maxilla length in C. nasus. The direct sequencing method was used to screen and analyze single nucleotide polymorphism (SNP) loci, analyze the genotype of each locus, and calculate the basic genetic parameters, genotype frequency, and gene frequency of each locus. Subsequently, association, linkage disequilibrium, and diplotype analyses were performed between these screened SNP loci and C. nasus maxillary length traits. The results showed that a total of five SNP loci were excavated in the Edn1 gene of C. nasus, including T134C, A418C, G1322A, C1607T, and A1636C. The two loci G1322A and A1636C are in linkage disequilibrium. Association analysis results showed that there was a significant correlation between T134C and A418C loci and maxilla length traits. Diplotype analysis showed that T134C and A418C loci formed diplotype D3 (heterozygous TC and Homozygous AA), which had significantly longer maxilla lengths than D1 (homozygous TT and heterozygous AC) and D2 (homozygous TT and homozygous CC). In addition, the Pearson correlation coefficient r=0.41 for the mouth-opening height/head length and maxilla length/head length of C. nasus. These findings indicate that the T134C and A418C loci were the dominant loci for the maxilla length of C. nasus, and the diploid D3 was the dominant genotype. This study can provide a scientific foundation for the candidate markers for molecular marker-assisted selection of the C. nasus with long maxilla.