Organellar genomes of liverworts are considered as one of the most stable among plants, with rare events of gene loss and structural rearrangements. However, not all lineages of liverworts are equally explored in the field of organellar genomics, and subclass Pellidae is one of the less known. Hybrid assembly, using both short- and long-read technologies enabled the assembly of repeat-rich mitogenomes ofPelliaandApopelliarevealing extraordinary reduction of length in the latter which impacts only intergenic spacers. The mitogenomes ofApopelliawere revealed to be the smallest among all known liverworts—109 k bp, despite retaining all introns. The study also showed the loss of onetRNAgene inApopelliamitogenome, although it had no impact on the codon usage pattern of mitochondrial protein coding genes. Moreover, it was revealed thatApopelliaandPelliadiffer in codon usage by plastome CDSs, despite identicaltRNAgene content. Molecular identification of species is especially important where traditional taxonomic methods fail, especially within Pellidae where cryptic speciation is well recognized. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. Application of super-barcodes, based on complete mitochondrial or plastid genomes sequences enable identification of all cryptic lineages withinApopelliaandPelliagenera, however in some particular cases, mitogenomes were more efficient in species delimitation than plastomes.