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The passion fruit (Passiflora edulis Sims), also called as ‘Baixiang-guo’, has been widely studied and grown, becoming the new darling of the fruit market throughout southern China. In the present study, we found the complete mitochondrial genome of the yellow passion (Passiflora edulis Sims. f. flavicarpa Deg.) fruit to be 680,480 bp in length. A total of 74 genes were predicted, including 41 protein-coding genes, 3 ribosomal RNA genes, and 30 transfer RNA genes. Under phylogenetic analysis, yellow passion fruit clustered with Populus davidiana, which further confirmed the traditional classification.