Peanut (Arachis hypogaea L.), one of the main oil and cash crops in the world, is easily susceptible to Aspergillus flavus, resulting huge loss in its quality, so Aspergillus flavus infection greatly limits peanut production and industry in China. Therefore, it is imperative to develop new peanut germplasm with resistance to Aspergillus flavus in breeding program. The core collection is well accepted as a useful way to improve the efficiency of crop germplasm evaluation and utilization, which contains a subset of accessions from the entire collection that covers the most of available genetic information. In the present study, a total of 561 accessions of Chinese peanut core collection and 155 accessions of ICRISAT mini core collection were identified. Eight varieties with resistance to Aspergillus flavus invasion and aflatoxin production each were developed, including one (51002-6) with elite agronomic traits. The peanut germplasm with resistance to Aspergillus flavus invasion and aflatoxin production in ICRISAT mini core were more than those in Chinese peanut core collection. In addition, the percentages of accessions with resistance to Aspergillus flavus invasion in var. hypogaea, and accessions resistant to aflatoxin production in var. hirsuta were relatively high in comparison with others. Genetic diversity in the resistant peanut selections was evaluated based on morphological traits and SSR approach. ICG12625 with resistance to aflatoxin production and ICG4750 with resistance to aflatoxin invasion were evaluated by SSR, the genetic distance of them with high-yielding cultivars such as Zhonghua 5, Zhonghua 6 and Zhonghua 12 and Yuanza 9102 was larger. The primers were designed based on the conserved NBS-LRR domains of the disease resistance genes sequence, one RGA (Resistance gene analog) from genomic DNA of six different peanuts with resistance to Aspergillus flavus was obtained through PCR.