A total of 74,403 bread wheat breeding lines from the year 2013-2020 developed by the International Maize and Wheat Improvement Center (CIMMYT) was genotyped. We used genotyping-by-sequencing (GBS) to construct 433 GBS libraries which were sequenced in the Illumina platform to generate 440 FASTQ files. The key file consists of metadata such as sample name, flowcell, lane number, and barcode used for multiplexing samples. The FASTQ file of corresponding samples can be identified based on the library. The raw reads are available at National Center for Biotechnology Information (NCBI) with BioProject accession PRJNA498085.