This paper introduces a robust and simple genotyping-by-sequencing (GBS) approach for high-diversity species, such as maize and barley. The method involves reducing genome complexity using restriction enzymes (REs) to target specific regions of the genome, avoiding repetitive sequences and focusing on lower copy regions. This approach simplifies computational alignment problems and is highly reproducible. The procedure is demonstrated with maize and barley populations, mapping approximately 200,000 and 25,000 sequence tags, respectively. The GBS method is advantageous for species lacking a complete genome sequence, as it can develop a reference map around restriction sites during sample genotyping. The tags can also be treated as dominant markers for kinship analyses without a reference genome. The authors highlight the potential of GBS for breeding, conservation, and global species surveys, enabling genomic selection and population structure determination without prior molecular tools.This paper introduces a robust and simple genotyping-by-sequencing (GBS) approach for high-diversity species, such as maize and barley. The method involves reducing genome complexity using restriction enzymes (REs) to target specific regions of the genome, avoiding repetitive sequences and focusing on lower copy regions. This approach simplifies computational alignment problems and is highly reproducible. The procedure is demonstrated with maize and barley populations, mapping approximately 200,000 and 25,000 sequence tags, respectively. The GBS method is advantageous for species lacking a complete genome sequence, as it can develop a reference map around restriction sites during sample genotyping. The tags can also be treated as dominant markers for kinship analyses without a reference genome. The authors highlight the potential of GBS for breeding, conservation, and global species surveys, enabling genomic selection and population structure determination without prior molecular tools.