The Mediterranean fan worm, Sabella spallanzanii (Gmelin, 1791), is a highly invasive pest species introduced to Australia and New Zealand, with the ability to alter marine ecosystems by outcompeting native species for food and space. Sabella spallanzanii has been established in southern Australia for decades, but was discovered in Botany Bay (NSW, eastern Australia) in 2013. In New Zealand, S. spallanzanii was first detected in March 2008. Using cytochrome c oxidase subunit 1 (COI) sequences, we investigate the phylogeography of the Australian and New Zealand populations of S. spallanzanii, including the possible origins of the recent incursions in both countries. Australian and New Zealand S. spallanzanii show minimal genetic diversity (0.2% divergence) and were dominated by two main haplotypes suggesting a commonality. Our molecular data are insufficient by themselves to identify fine-scale invasion pathways in antipodean S. spallanzanii, but the similar, minimal haplotype diversity in combination with well-constrained field survey data suggests that the New Zealand incursion originated from southern Australia, rather than as a new incursion from the Mediterranean Sea. This highlights the importance of ongoing marine biosecurity surveillance and monitoring as well as improvements to biosecurity protocols for international and domestic vessels. The origin of the eastern Australian (Botany Bay) incursion is plausibly derived from either southern Australia or as a ‘return’ from New Zealand, and requires further, more detailed investigation.