Friesea grisea is the only springtail species currently described from both East (Victoria Land) and West Antarctica (Antarctic Peninsula), although levels of genetic divergence between the two regions suggest the possibility of cryptic species. Determining the genetic structure of populations in the two regions is necessary in order to compare the effects of the different environmental conditions in the two regions, the different evolutionary histories of their inhabitants, and for assessing any influence of latitude in each region on genetic diversity. We analysed sequences of the mitochondrial COX1 and ATP6 genes from a total of 111 individuals for 17 sites (nine on the Antarctic Peninsula and eight in Victoria Land), to assess levels of genetic diversity. Both regions have their own unique sets of haplotypes, differing by about 20% of their nucleotide sequences. A similar number of haplotypes was found in the two regions, and within each we found two groups of populations sharing no haplotypes. In the Antarctic Peninsula, two, presumably ancestral, haplotypes are dominant in frequency. In Victoria Land, the Cape Hallett population showed a distinct set of haplotypes, genetically different from the southernmost populations, suggesting differentiation on pre-Pleistocene timescales.