Haplolepideous moss systematics has been through major changes based on morpho-molecular studies. However, many taxa remain little studied with still unclear circumscriptions and relationships among the traditionally recognized families. We inferred the phylogenetic relationships of the haplolepideous mosses based on a sample of 37 out of the 38 haplolepideous moss families and using mitochondrial (nad5 G1 intron) and chloroplast (trnS-rps4 spacer/rps4 gene and trnL gene/trnL-trnF spacer) markers. The resolved relationships indicate the need for rearrangements in the circumscription of the Aongstroemiaceae and Dicranellaceae and their genera, which correspond to the variation of morphological characters of leaf shape, rhizoid tuber morphology, and capsule and peristome traits. The two families, although historically considered morphologically close, were resolved as separate lineages in the core haplolepideous clade. The genera Aongstroemia and Dicranella were resolved as polyphyletic across the clades corresponding to the families Aongstroemiaceae and Dicranellaceae and other clades. The characterization of Aongstroemia by julaceous plants is not supported; the three species sampled here belong in three separate families and differ from one another in other (more stable) characters, such as the presence and shape of peristome teeth. Regarding Dicranella, the sampling of 13 of its 167 species suggests the broad morphological variation comprised by the genus under its current circumscription might be narrowed down to smaller ranges corresponding to the phylogenetically separate clades. The present molecular data furthermore suggest changes in the composition of the protohaplolepideous Dicranidae grade, including one Dicranella clade, a new lineage with a ditrichoid morphology, but excluding the Chrysoblastellaceae, which were resolved in the core haplolepideous clade. The latter finding implies the independent evolution of the rare double-opposite peristome type in both the protohaplolepideous grade and the core haplolepideous clade. Keywords haplolepideous mosses; nad5 G1 intron; polyphyly; phylogenetics; trnS-trnF Supporting Information may be found online in the Supporting Information section at the end of the article.

The use of molecular data to study the evolutionary history of organisms has revolutionized the field of systematics. Now with the appearance of high throughput sequencing (HTS) technologies, more and more genetic sequence data are available. One of the important sources of genetic data for phylogenetic analyses has been mitochondrial DNA. The limitations of mitochondrial DNA for the study of phylogenetic relationships have been thoroughly explored in the age of single locus phylogenetic studies. Now with the appearance of genomic scale data, increasing number of mitochondrial genomes are available, leading to an increasing number of mitophylogenomic studies. Here, we assemble 47 mitochondrial genomes using whole genome Illumina short reads from representatives of the family Erebidae (Lepidoptera), in order to evaluate the accuracy of mitochondrial genome application in resolving deep phylogenetic relationships. We find that mitogenomes are inadequate for resolving subfamily‐level relationships in Erebidae, but given good taxon sampling, we see its potential in resolving lower level phylogenetic relationships.