Many agronomic traits are difficult to select in Arachis hypogaea L. by conventional selection techniques, and marker-assisted selection offers an additional tool for obtaining improved germplasm lines. Molecular markers allow more efficient selection and offer a mechanism to eliminate undesirable traits associated with hybridizing diverse genotypes. The cultivated peanut has been analyzed by several marker systems, including RFLPs, RAPDs, AFLPs, and SSRs. Variation has been observed among diverse genotypes in approximately 5% of the markers analyzed, but the number is much lower between pairs of A. hypogaea lines. Conversely, a large amount of variation has been observed among Arachis species. Molecular maps have been constructed independently in two laboratories by utilizing Arachis species; however, a map of the cultivated peanut will be very difficult and costly to produce. Studies of advanced-generation inter-specific hybrids have shown that A. cardenasii genes can be incorporatead into most linkage groups of A. hypogaea, indicating that A. hypogaea is not an allotetraploid in the classical sense where chromosomes from donor species are nonhomologous. Other molecular studies have identified A. duranensis and A. ipaensis as likely progenitor species of A. hypogaea. Associations of molecular markers with genes conditioning disease and insect resistances have been detected, and these investigations are beginning to be productive for selecting improved breeding lines and cultivars of peanut.