In order to infer the origin and the evolution of Antarctic Collembola, a correct phylogenetic analysis depicting relationships among Antarctic and non-Antarctic species is required. A preliminary assessment of the value of DNA sequences in reconstructing phylogenetic relationships among the Antarctic Isotoma klovstadi and other non-Antarctic species was carried out by sequencing one mitochondrial gene (Cytochrome c oxidase, subunit II) and two nuclear genes (a fragment of the 28S rDNA and the Elongation Factor-1α). Estimates of base composition heterogeneity revealed that in the two protein-coding genes (COII and EF-1α) 3rd codon position sites are compositionally very heterogeneous and the analysis of these two genes was therefore performed only on 1st and 2nd codon position sites. Phylogenetic analyses using Maximum Likelihood, Maximum Parsimony and Minimum Evolution revealed that the COII and the EF-1α genes are more suitable than the D3 fragment for the reconstruction of phylogenetic relationships within the Family Isotomidae to which Isotoma and several other genera of Antarctic Collembola belong.