Genotyping-By-Sequencing (GBS) is rapidly gaining popularity for high throughput applications in livestock genetics and agriculture biotechnology.  Ion Ampliseq^TM is a highly multiplexed, PCR-based resequencing technology that enables the targeting of hundreds to thousands of markers across hundreds of samples in a single sequencing run using the Ion Torrent^TM Sequencing.  We recently demonstrated the power of Ion Ampliseq^TM GBS for high throughput cattle genotyping.  We designed Ion Ampliseq^TM primers targeting over 4800 bovine SNP markers as a single pool, and developed a simple, low cost, high throughput and rapid protocol ideal for commercial testing environments.  The data showed excellent reproducibility, accuracy and >95% concordance with existing microarray data even at high (384) sample multiplex.  Ion Ampliseq^TM offers the flexibility to design customized GBS panels for any species with a reference genome, and with little to no optimization required.