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Genotyping platforms provide robust support for genomics, genetics, and molecular breeding. Given the economic importance of cotton, it is urgent to develop a cotton genotyping platform that features high throughput, precision, efficiency, and cost-effectiveness. Here we reported the development of a liquid SNP chip named “ZJU CottonSNP40K” through genotyping by target sequencing, along with its utility. Representative SNPs of this chip were selected by screening more than 3,828,396 SNPs extracted from the abundance of resequencing data available from nearly 1000 cotton accessions. After strict selection, the final array includes 40,071 core SNPs evenly distributed across 26 chromosomes, 27.64 % of which are within genic regions. Testing on 13 cotton accessions showed the chip has high genotyping efficiency and accuracy. The SNP array was further used to genotype 328 (TM-1 × latifolium)F₂ …