The current primary threats to biodiversity on a global scale are species invasions and habitat modification. Management of vulnerable populations often involves a lengthy sequence of 1) research to identify threats and recommend management strategies, 2) active management, and 3) results monitoring to assess effectiveness of management. The last mainland population of the large, endemic New Zealand skink (Whitaker's skink [Cyclodina whitakeri]) provides an opportunity to test this process in a system where the synergistic effects between invasive species (introduced rodents and grasses) have predicted outcomes. A low abundance of Whitaker's skink at the Pukerua Bay Scientific Reserve in the 1980s prompted management recommendations to remove grazing stock and revegetate the site to simultaneously restore habitat and provide protection against introduced mammalian predators. Since Whitaker's skink have low detectability, it was recommended that sympatric copper skink (C. aenea) be used an indicator species of management effectiveness. Grazing stock were removed in 1987, but efforts to revegetate the site were ineffective. Long-term monitoring (1984–2006) of the Whitaker's skink population and 4 other sympatric lizard species within a 336-m² area at the site resulted in 1,693 lizard captures over 7,597 trap days. Whitaker's skink represented 2.8% of all captures in 1984–1988, but declined relative to other species to represent only 0.2% of captures in 2000–2006 (representing 2 individuals). Congeneric copper skink showed a similar decline with capture rates also approaching zero by 2006. Removing grazing stock did not result in an increased abundance of Whitaker's skink or copper skink through improved habitat quality, as was intended by the management recommendation. Instead, reduced grazing has allowed introduced seeding grasses to proliferate, which may have led to periodic rodent irruptions, supporting a guild of introduced mammalian predators and depleting populations of Whitaker's skink and copper skink. In this instance, attempted protection may have driven a vulnerable population towards extinction. We recommend investigating the feasibility of constructing a mammal-proof fence around the core Whitaker's skink habitat, as the last remaining management option to salvage the population.