The cultivated peanut is a major edible oilseed crop. Remarkable success has been achieved in breeding new peanut varieties. The narrow genetic base of the cultivated peanut, as the result of a series of six bottlenecks in evolution, however, makes it increasingly difficult to develop breakthrough varieties solely by intraspecific hybridization. For this reason, research has been carried out to exploit incompatible wild Arachis species. In this paper, we report for the first time a genetic diversity assessment of 30 progenies from intersectional crosses between high-oleic peanut cultivar Huayu 665 and two wild species, A. paraguariensis or A. appresipilla, together with 32 cultivar materials, and 29 wild accessions using transposon element markers. The hybrids had higher genetic diversity than the cultivars, broadening the genetic base of peanut breeding. Hybrid progenies with improved insect pest resistance and both high oleic acid and high oil/protein were obtained. Hopefully, peanut varieties with high and stable yield and quality will be bred using crop wild relatives in the near future.