Arachis kuhlmannii occurs in Mato Grosso and Mato Grosso do Sul States, Brazil. Its area of occurrence partially overlaps with that of other species in the Arachis section. Because of their morphological similarities, these species are often mistaken one for another. This study aimed the correct classification of available accessions as Arachis kuhlmannii, or other species, and the characterization of similarities among accessions and Arachis hypogaea by morphological, cytogenetic, and molecular marker analyses. Thirty-eight accessions were used. Principal component analysis was used for morphological characterization, root tips for mitotic metaphase analysis, and RAPD markers for molecular characterization. Cluster analysis discriminated accessions with the A genome from the B genome. Cluster analysis based on molecular markers discriminated natural populations in a manner that correlated with geographical areas of the collection. Arachis cardenasii and A. hypogaea were isolated from other A-genome accessions. Cytogenetic analyses confirmed the existence of diagnostic characteristics that distinguish species with the A genome from those with the B genome. Results suggest the need for a taxonomic review of some species in the Arachis section, as we could not discriminate as distinct species all of the accessions identified as A. kuhlmannii, A. helodes, and A. simpsonii by using morphological, molecular, and cytogenetic markers.