Cordycepsis a diverse genus of insect pathogenic fungi, with about 180 accepted species, including some well-known ones used as ethnic medicine and/or functional food. Nevertheless, mitogenomes are only available for four members of the genus. The current study reports the mitogenome ofCordyceps blackwelliae, a newly described entomopathogenic fungus. The 42,257-bp mitogenome of the fungus encoded genes typically found in fungal mitogenomes, and a total of 14 introns inserted into seven genes, includingcob(1 intron),cox1(4),cox3(3),nad1(1),nad4(1),nad5(1), andrnl(3). RNA-Seq analysis revealed differential expression of mitochondrial genes and supported annotations resulting from in silico analysis. There was clear evidence for polycistronic transcription and alternative splicing of mitochondrial genes. Comparison among mitogenomes of five differentCordycepsspecies (i.e.,C. blackwelliae,C. chanhua,C. militaris,C. pruinosa, andC. tenuipes) revealed a high synteny, with mitogenome size expansion correlating with intron insertions. Different mitochondrial protein-coding genes showed variable degrees of genetic differentiation among these species, but they were all under purifying selection. Mitochondrial phylogeny based on either nucleotide or amino acid sequences confirmed the taxonomic position ofC. blackwelliaein Cordycipitaceae, clustering together withC. chanhua. This study promotes our understanding of fungal evolution inCordyceps.Supplementary InformationThe online version contains supplementary material available at 10.1186/s43008-023-00118-5.