This study aimed to identify genetic variation in peanut genome,clarify their distribution characteristic,develop and verify InDel markers, and evaluate the efficiency of InDel markers in peanut cultivar identification. Genome resequencing data of 13 peanut cultivars were used to identify genome-wide variations, and a total of 313,432 high-quality SNPS and 38,777 high-quality InDel were detected, with an average distribution density of 123 and 15.23 /Mb, respectively. The InDels and SNPs were mainly distributed in intergenic regions, with a frequency of 52.35% and 60.08%, respectively, followed by upstream and downstream gene sequences, accounting for 36.12% and 32.49%. Primers were designed using InDel with insertion or deletion length ≥10 bp, and 3,675 InDel could be used to develop InDel markers. These InDel locus were unevenly distributed on the 20 chromosomes of peanut, and the marker density ranged from 1.08 (Chr02) to 2.45 (Chr08), with an average of 1.48 /Mb. Using electronic PCR, 2561 pairs of primers (69.69%) amplified 1~3 effective loci in the peanut reference genome. The physical map of amplification loci was drawn according to the loci position in cultivated peanut genome. Among 100 pairs of random primers, 31 pairs amplified different bands in the 4 varieties with distant relatives. The 31 InDel primer pairs amplified 62 alleles in 47 peanut varieties (or breeding lines), the frequency of major genes ranged from 0.51 to 0.98 with an average of 0.77, and the PIC information ranged from 0.04 to 0.37, with an average of 0.24. Both cluster analysis and population structure analysis could divide the 47 peanut varieties (or breeding lines) into two groups, and the 47 materials could be distinguished by at least 7 markers, indicating that the developed InDel markers could be effectively used for the assessment of genetic diversity and variety identification of peanut. The research results enriched the molecular markers of peanut, and provided a theoretical basis for the use of InDel markers in genetic studies of peanut resource genetic diversity, variety identification, fingerprint construction.