The invention discloses a SNP (Single Nucleotide Polymorphism) primer for screening fugu rubripes seedlings and a screening method, which are capable of saving manpower and material resources, lowering seed screening cost and guaranteeing excellent characters of the filial generation. The sequence of the SNP primer is as shown in SEQ ID NO.1 and SEQ ID NO.2. The seedling screening method comprises the following steps: extracting the genomic DNA of to-be-detected fugu rubripes; taking the acquired genomic DNA as a template; performing PCR amplification with upstream primer and downstream primer, thereby obtaining a PCR product; sequencing and genetically typing the obtained PCR product; screening the fugu rubripes with DNA sequence as shown in SEQ ID NO.3 and the No.591 locus gene started from 5' end being homozygosis TT.