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Morchella eohespera Beug, Voitk & O’Donnell is a typical black morel species. In this study, using the Nanopore sequencing platform, we characterized its whole mitochondrial (mt) genome sequence. Mt genome of M. eohespera is composed of circular DNA molecules of 243,963 bp, which encoded 102 protein-coding genes (PCGs), two ribosomal RNA genes (rRNA), and 31 transfer RNA (tRNA) genes. The base composition of M. eohespera mitogenome is as follows: A (30.40%), T (29.30%), G (20.8%), and C (19.5%). The phylogenetic analysis suggested that M. eohespera was closely related to the congeneric M. importuna.