As the cost for next-generation-sequencing (NGS) goes down, NGS-based genotyping is becoming a routine in many crop breeding programs in the U.S. Previously, genotyping-by-sequencing (GBS) has been widely used in crop genetic research, however, this technology has been patented that restricts its use in breeding. To explore new NGS-based genome-wide marker platform for breeding, we developed a method called multiplex restriction amplicon sequencing (MRASeq) to sequence amplicons within restriction sites using two-step PCR without enzyme digestion and adaptor ligation seen in GBS. We first conducted ‘in-silico digestion’ of target species with three enzyme pairs (PstI-MspI, HinfI-CviAII, and ApekI) frequently used for GBS in different species, ranked primer sets based on their amplicon counts using two algorithms (distal or complete genome counts), and then selected 48 primer pairs with the most amplicon counts for library construction. By adding appropriate barcodes and adapters for the Illumina sequencer, hundreds of plant samples can be multiplexed in a single sequencing run. Using MRAseq, we generated thousands of high-quality SNPs in a wheat breeding panel, which are sufficient for genomic selection. We also extended this approach to other crop species including barley, sorghum, soybeans, corn, pearl millet and generated reasonably high amplicon counts using just 48 primer pairs depending on species and genome size. The low cost, uniform distribution in the genomes of various species and simplicity make MRAseq an attractive genotyping tool for genomic selection in most crop species.