Endogenous viral elements (EVEs) of four distinct badnavirus species were previously partially characterized in the genome of African yam (Dioscorea cayenensis and D. rotundata), using molecular approaches. In order to fully elucidate the structure of badnaviral EVEs in African yams, the genomes of accessions 'Ti Guinée' (D. cayenensis) and 'Msg 5' (D. rotundata) were sequenced using HiFi PacBio high-throughput sequencing (HTS) and searched for badnavirus EVEs. Large contigs of up to 50 Mbp were assembled and combined with optical maps produced by Saphyr system (Bionano), resulting in two high-quality reference sequences for Dioscorea. Twelve and six contigs originating from the genomes of 'Ti Guinée' and 'Mgs 5', respectively, contained badnaviral EVEs ranging in size between 124.4 and 17.7 kbp. All badnaviral EVEs were highly rearranged, especially those of D. cayenensis, which were also larger, and most contained interspersed sequences originating from distinct badnavirus species or from viruses in different Caulimoviridae genera. One EVE from accession 'Ti Guinée' contained badnaviral sequences surrounded by putative Geminiviridae sequences. Several EVEs from 'Ti Guinée' contained sequences of a yet unreported Caulimoviridae closely related to but distinct from Dioscorea nummularia-associated virus (DNUaV; Dioscovirus). Several EVEs originating from either species contained more-than-length copies of badnaviral genomes that may be replication competent and infectious.