Black point is a serious threat to wheat production and can be managed by host resistance. The availability of molecular markers will accelerate the improvement of black point resistance in wheat breeding. In the present study, we performed a linkage analysis in the Linmai 2/Zhong 892 recombinant inbred line (RIL) population and a genome-wide association study (GWAS) in 166 elite wheat cultivars to better understand the genetic basis of black point resistance and identify linked markers. A high-density linkage map was constructed by genotyping the RILs with the wheat 90K single nucleotide polymorphism (SNP) chip, and 166 wheat cultivars were genotyped with the wheat 90K and 660K SNP arrays. Composite interval mapping detected nine quantitative trait loci (QTL), designated as QBp.caas-2AL, QBp.caas-2BL, QBp.caas-3AL, QBp.caas-3BL, QBp.caas-5AS, QBp.caas-6A, QBp.caas-7AL.1, QBp.caas-7AL.2 and QBp.caas-7BS, respectively, explaining 3.7% to 13.4% of the phenotypic variances. With the GWAS of 166 wheat accessions, 25 loci were identified on chromosomes 2A, 2B, 3A, 3B (2), 3D, 4B (2), 5A (3), 5B (3), 6A, 6B, 6D, 7A (5), 7B and 7D (2), respectively, explaining the phenotypic variances ranging from 7.9% to 18.0%. Six loci were observed in both the linkage analysis and GWAS, indicating that the linkage mapping and GWAS are complementary in identifying genes. Among the co-localized loci, QBp.caas-2AL overlapped with the gene Ppo-A1, which encodes peroxidase, indicating that the black point can be caused by enzymatic browning following stress. By fine mapping, the genetic region of QBp.caas-3BL was narrowed down to a physical interval of approximately 1.7 Mb, including five high-confidence annotated genes. Linear regression showed a clear dependence of black point scores on the number of favorable alleles, suggesting that QTL pyramiding will be effective to increase black point resistance. This study provides new insights into the genetic architecture of black point reaction and provides available germplasm and molecular markers for wheat black point resistance breeding.