Recent advances in next generation sequencing technology have increased the output/cost to a level that now allows for the potential of GBS in livestock. We have explored GBS in sheep with the aim of developing a cost effective, reproducible and high-throughput SNP genotyping method that can be manipulated to return varying genome coverage. Restriction enzymes have been employed together with adapter based multiplexing for next generation sequencing, a technique that has been well established for high-density SNP discovery and genotyping in numerous species. We utilised the GBS method described by Elshire et al., 2011 (PLoS ONE 6:e19379), however, through the addition of specific nucleotides within and following the restriction enzyme cut site to the common adapter we are able to reduce the complexity of the genome in a controlled manner. Varying the number of samples and the ‘size’ of the reduced genome per lane on an Illumina HiSeq2000 allows for differing magnitudes of SNPs to be genotyped and interrogated. The method for reducing the complexity of the genome, sequencing and bioinformatics pipeline for GBS in sheep will be presented.