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Complete plastomes of 14 African yam species were reconstructed from whole genome sequencing. These plastomes sizes varied from 151,908 to 155,155 bp. We predicted 130 genes, including 18 duplicated genes located in the two inverted regions. Phylogenetic analysis obtained using the maximum likelihood procedure revealed that each species was distinct with high support. This resource will be useful for phylogenetic and diversity analysis of Dioscorea species.