Burrowing sea anemones have a simple morphology with an elongate body and a round aboral end that anchors the animal into the sediment leaving only the tentacle crown exposed. Despite the general polyphyly of burrowers within Actiniaria (formerly athenarians), a monophyletic clade of burrowing anemones has been recently discovered in Antarctica (Scytophorus + Halcampulactis+ Halcampoides). Based on phylogenetic analyses using nuclear and mitochondrial markers (12S, 16S, 18S, 28S, COIII) as well as morphology and cnidae, this clade has been putatively classified within Actinostoloidea but its position is unstable and support is low. Superfamily Actinostoloidea is the second most speciose in Antarctica, having a long and complex taxonomic history with more than half of its genera narrowly defined and monotypic. This pattern may be the result of relictual distributions shaped by glacial periods, colonization of the Southern Ocean several times at different periods or independently from different ocean basins at the same time, or polar emergence from the deep sea following the retreat of multiyear sea ice in interglacial periods with subsequent speciation in the Antarctic shelf. To improve resolution and help to establish the position of the recently discovered deep-sea, Antarctic lineage of burrowing sea anemones, we generated complete mitogenomes for five actinostoloideans, including three representatives of this clade, and combined them to the 29 available sea anemone mitogenomes. Based on our ML phylogenetic reconstruction for the Order Actiniaria, we evaluate the position of the clade in question, the resurrection and circumscription of family Halcampoididae to accommodate it, and implications for the evolution of burrowing sea anemones.