We have developed a new method for generating single nucleotide polymorphisms (SNPs) using next-generation sequencing. RAD Sequencing has become an established method for SNP genotyping on Illumina sequencing platforms. With a modification to the double-digest RAD Sequencing methodology on Illumina, we have developed a protocol and new adapters for using Ion Torrent semiconductor sequencing. To validate and demonstrate the method, we sequenced 13 genomic libraries of three non-model vertebrate species (two fishes and a lizard).