Insertion/deletion (InDel) is the second largest molecular markers, which provide the valuable reference for population genetics and marker-assisted selection study. Peanut is one of the most important oil crops worldwide. The whole genome sequence of cultivated peanut has been released and therefore provided the important genome reference for functional genomic studies. In this study, by taking use of the genotyping-by-sequencing datasets on 169 peanut core collections, we identified 10,401 InDels with the size difference of 1 to 14 bp. The highest number of InDels was observed on chromosome Arahy.16, while the lowest number was found on Arahy.08. Although only 1,167 Indels were located in coding regions, obviously these InDels might show the specific functions, including catalytic activity and binding compared with other regions. The KEGG analysis suggested that InDels were mainly detected in the metabolism process. These InDels explored in this study might serve as the important genetic resources being useful for the further validation of functional genes.