A new wave of agricultural intensification in New Zealand is causing increasing pressure on natural resources. Moller et al. (2008) suggest that the agricultural intensification is inevitable, that negative environmental impacts have only been demonstrated for aquatic systems, and that a new paradigm based on integrating indigenous biodiversity and agriculture offers the best way forward. We question all these assertions. Recent agricultural intensification is increasingly driven by international economic opportunities for agricorporates to maximise returns. Intensification over the last two decades is causing loss of habitat for indigenous species and homogenisation of landscapes at scales unprecedented since deforestation by colonial farmers. Regional and district councils appear ill prepared for a formative role requiring sustainable land and resource use, while current patterns of local consumption and offshore resource subsidisation for agribusinesses are probably unsustainable. Irrespective of the drivers of agricultural intensification, residual indigenous biodiversity in agricultural landscapes in New Zealand is on an extinction pathway. The challenge for agro-industry is to demonstrate that it can, in the absence of regulation, use natural resources and at the same time facilitate persistence of indigenous biodiversity components at scales that contribute to national biodiversity goals.