The present genetic diversity of commensal rodent populations is often used to inform the invasion histories of these species, and as a proxy for historical events relating to the movement of people and goods. These studies assume that modern genetic diversity generally reflects early colonising events. We investigate this idea by sequencing the mitochondrial DNA of rodent bones found in a 19th-century archaeological site in The Rocks area of Sydney, Australia, the location of the first historical European port (Port Jackson) in Australasia. We also interpret the history of rodent invasions in New Zealand based on this evidence, as Sydney was the primary port from which European boats sailed to New Zealand. We identified 19th-century bones from two species, Norway rats ( Rattus norvegicus ) and house mice ( Mus musculus domesticus ). We found six historical genetic haplotypes in the 39 Norway rats, showing either multiple early introductions or a diverse initial founding population. One of them was identical with Norhap01 common in the North Island of New Zealand, but none was like the haplotype Norhap02 found throughout the South Island. We found three haplotypes in seven house mice, all belonging to the dominant subspecies established in Australia, M.m. domesticus . We had few modern Norway rat and house mouse DNA sequences from Sydney, but those we had did tentatively support the hypotheses that (1) modern samples can represent at least a preliminary estimate of historical diversities and origins, and (2) Asian haplotypes of both Norway rats and of house mice reached the South Island of New Zealand early in colonial times direct from China rather than through Port Jackson.