Members of the Moelleriella (Hypocreales, Clavicipitaceae) genera are insect pathogens with specificity for scale insects and whiteflies. However, no mitochondrial genomes are available for these fungi. Here, we assembled seven mitogenomes from M. zhongdongii, M. libera, M. raciborskii, M. gracilispora, M. oxystoma, Moelleriella sp. CGMCC 3.18909 and Moelleriella sp. CGMCC 3.18913, which varied from 40.8 to 95.7 Kb. Synteny and codon usage bias was relatively conserved; with the mitochondrial gene arrangement completely homologous to the gene order of 16 other species within the Hypocreales. However, extensive intron polymorphism exists between Moelleriella species. Evolutionary analyses revealed that all 15 core protein coding genes had ka/ks < 1, indicating purifying selection pressure. Sequence variation within the mitochondrial ribosome protein S3 (rps3) gene showed the largest genetic distance with the NADH dehydrogenase subunit 4L (nad4L) showing the smallest. Comparative mitogenomic analyses showed that introns were the main factor contributing to the size variation of Moelleriella and more widely in Hypocreales mitogenomes. Phylogenetic analyses indicate that the seven Moelleriella species examined form a well-supported clade, most closely related to Hypocrella. These data present the first mitogenome from Moelleriella and further advance research into the taxonomy, origin, evolution, and genomics of Moelleriella.