Mitochondrial DNA sequences from the ND2 gene were used to investigate the systematic relationships within pygmy possums (Cercartetus) at the subspecies and species level. The phylogenetic relationships identified between Cercartetus species using partitioned ND2 sequences are in agreement with published morphological characters. C. caudatus was identified as the basal member of this assemblage, whilst C. nanus and C. concinnus are linked to the exclusion of C. lepidus. Molecular data identifies some inconsistencies in the assignment of subspecies within Cercartetus, suggesting that revision may be warranted.