Peanut (Arachis hypogaea L.) is an important oilseed crop and food legume that is highly susceptible to biotic and abiotic factors. Wild Arachis species represent useful genetic resources because of their resistance to pests and diseases. In particular, understanding the affinity between B-genome species is important for broadening the genetic base of A. hypogaea (AABB genome), since only one population of A. ipaënsis is known, and relatively few other species have been described. Therefore, we aimed to determine the genomic affinity between A. ipaënsis and A. williamsii by developing hybrids. Microsatellite markers verified the hybrid status, and chromosome pairing and pollen viability results revealed that the species share high genomic affinity. Additionally, the presence of dyads detected in sporad and pollen analyses indicated the production of 2n gametes. These results will be useful for performing evolutionary studies and developing strategies for introgression programs to improve the B genome of A. hypogaea.