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<i>Apostasia fujianica</i> belongs to the genus <i>Apostasia</i> and is part of the basal lineage in the phylogenetic tree of the Orchidaceae. Currently, there are only ten reported complete mitochondrial genomes in orchids, which greatly hinders the understanding of mitochondrial evolution in Orchidaceae. Therefore, we assembled and annotated the mitochondrial genome of <i>A. fujianica</i>, which has a length of 573,612 bp and a GC content of 44.5%. We annotated a total of 44 genes, including 30 protein-coding genes, 12 tRNA genes, and two rRNA genes. We also performed relative synonymous codon usage (RSCU) analysis, repeat sequence analysis, intergenomic transfer (IGT) analysis, and Ka/Ks analysis for <i>A. fujianica</i> and conducted RNA editing site analysis on the mitochondrial genomes of eight orchid species. We found that most protein-coding genes are under purifying selection, but <i>nad6</i> is under positive selection, with a Ka/Ks value of 1.35. During the IGT event in <i>A. fujianica</i>’s mitogenome, the <i>trnN</i>-<i>GUU</i>, <i>trnD</i>-<i>GUC</i>, <i>trnW</i>-<i>CCA</i>, <i>trnP</i>-<i>UGG</i>, and <i>psaJ</i> genes were identified as having transferred from the plastid to the mitochondrion. Compared to other monocots, the family Orchidaceae appears to have lost the <i>rpl10</i>, <i>rpl14</i>, <i>sdh3</i>, and <i>sdh4</i> genes. Additionally, to further elucidate the evolutionary relationships among monocots, we constructed a phylogenetic tree based on the complete mitogenomes of monocots. Our study results provide valuable data on the mitogenome of <i>A. fujianica</i> and lay the groundwork for future research on genetic variation, evolutionary relationships, and breeding of Orchidaceae.