Isolation and characterization of gene-derived single nucleotide polymorphism (SNP) markers in Scylla paramamosain

► We isolated and characterized the first set of SNPs in Scylla paramamosain. ► Thirty-seven SNPs were identified, of which twenty-four were genotyped successfully using SNaPshot. ► The total level of polymorphism of these SNP loci was relative low. ► No significant departures from HWE and no significant LD were found.