Previous work focused on allozymes and mitochondrial haplotypes has detected high levels of genetic variability between Cryptopygus terranovus populations, a springtail species endemic to Antarctica, until recently named Gressittacantha terranova. This study expands these biogeographical surveys using additional analytical techniques, providing a denser haplotype dataset and a wider sampling of localities. Specimens were collected from 11 sites across Victoria Land and sequenced for the cytochrome c oxidase subunit I mitochondrial gene (cox1). Haplotypes were used for population genetics, demographic, molecular clock and Bayesian phylogenetic analyses. Landscape distribution and clustering of haplotypes were also examined for the first time in this species. Only three (out of 67) haplotypes are shared among populations, suggesting high genetic structure and limited gene flow between sites. As in previous studies, the population of Apostrophe Island has a closer genetic similarity with those of the central sites, rather than with its neighbours. Molecular clock estimates point to early differentiation of haplotypes in the late/mid-Miocene, also supporting the view that C. terranovus is a relict species that survived on the Antarctic continent during the Last Glacial Maximum. The present genetic composition of populations represents a mixture of ancient and more recent haplotypes, sometimes occurring in the same localities