Here, we provide the first complete mitochondrial genomes for two higher taxa of Peracarida, Lophogastrida and Stygiomysida. We examined Lophogaster typicus as a representative of Lophogastrida and Spelaeomysis bottazzii as a representative of Stygiomysida. Both mitogenomes have all typical metazoan genes (13 protein‐coding genes, two ribosomal RNA genes and 22 transfer RNAs). The mitogenomes have a length of 15,076 bp in L. t...