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To enhance their conservation value, several hundred islands worldwide have been cleared of invasive alien rats, Rattus spp. One of the largest projects yet undertaken was on 43 km2 Henderson Island in the Pitcairn group, South Pacific, in August 2011. Following massive immediate mortality, a single R. exulans was observed in March 2012 and, subsequently, rat numbers have recovered. The survivors show no sign of resistance to the toxicant used, brodifacoum. Using pre and post-operation rat tissue samples from Henderson, plus samples from around the Pacific, we exclude re-introduction as the source of continued rat presence. Microsatellite analysis of 18 loci enabled comparison of genetic diversity of Henderson rats before and after the bait drop. The fall in diversity measured by allele frequency change indicated that the bottleneck through which the breeding population passed was probably around 50 individuals, representing a census population of about 60-80 animals. This is the first failed project that has estimated how close it was to success.