High throughput methods and kits for single nucleotide polymorphism (SNP) genotyping are provided. The methods involve utilizing nested PCR amplification reactions which produce sequencible and ligatible structures. An outer PCR primer set amplifies the SNP, and an inner PCR primer set amplifies a portion of the DNA amplified by the outer primer set, but does not amplify the SNP itself. The inner and outer primers may reaction include non-target common domain sequences, and the inner primer common domain sequences may comprise digestion restriction endonuclease recognition sites. The design of the inner primer set allows precise tailoring of the sequencible and ligatible structures with respect to length and base composition.