Analyses of mitochondrial DNA variation in archaeological samples of Rattus exulans obtained during the 1997 excavations at Emily Bay, Norfolk Island suggest a high degree of variation in the prehistoric populations on the island. The ten samples sequenced produced five unique haplotypes. This result is consistent with a scenario of multiple introductions of the species to the island. There are clear affiliations with East Polynesian and New Zealand samples, however other lineages also appear to be present on Norfolk Island. Three haplotypes that had previously not been identified in tropical East Polynesia appear on Norfolk. One of these has also been identified in an archaeological sample from New Zealand. The other two haplotypes have yet to be identified elsewhere.