Peanut (Arachis hypogaea L.), an important source of oil and protein, is native to South America. Most peanuts grown in Japan are large-grain cultivars that are eaten mainly as a snack. The peanut germplasm was introduced from abroad over a century ago and has been used for breeding. Although many peanut varieties have been developed, the relationship between Japanese varieties and peanut phylogeny remains unclear; therefore, this study assessed the diversity and genetic relationships within the peanut germplasms in Japan using allelic variation in a selected set of 13 SSR markers. We analyzed 201 accessions of A. hypogaea and 13 accessions of Arachis wild species: 13 primer pairs amplified 108 polymorphic alleles in A. hypogaea. The detected alleles were 3–15 at each of the 13 markers, with an average of 8.3 per marker. The phenogram based on the SSR genotypes was obtained. A. hypogaea and A. monticola made a separate group from diploid species; they were classified into 150 genotypes. A. hypogaea and A. monticola were divided further into two groups; the first group consisted mainly of spp. fastigiata accessions; the second group consisted mainly of spp. hypogaea accessions and tetraploid wild peanut A. monticola.