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The Mediterranean climate regions of Western Australia and South Africa are recognized as global hot spots of diversity. Both are threatened by climate changes that are projected to have significant impacts on the quantity and variability of rainfall and affect key ecosystem drivers (e.g. fire regimes). This poses significant challenges to monitoring programs designed to detect these impacts. Effective monitoring of the impact of climate change on biodiversity (rather than individual species) requires a cross-disciplinary, coordinated, focused and integrated approach. Ideally, this should involve a multidisciplinary team of specialists working to a common plan on the same set of plots. The contributions of 'citizen scientists' are potentially useful if well managed. Biodiversity per se (across all kingdoms of life, and including the levels of the gene, population and community) should be monitored, especially key species interactions and processes. Forestcheck is an example of such a program which has been applied in forests in south-west Western Australia since 2001. In concert with measuring the direct impact of climate change on biodiversity and the indirect impact of factors that affect biodiversity (such as disease, invasive species, fire regime and habitat removal), there is a need for a proactive focus on creating, maintaining and monitoring resilience to climate change impacts in ecosystems. It is also necessary to monitor the effectiveness of management actions such as vegetation thinning, changes in fire regimes, species translocations and revegetation of farmland to link isolated protected areas in agricultural landscapes, remnant native vegetation in rangelands and extensive protected areas. A pluralist approach is recommended. This should include natural experiments, matched photographs where available, passive adaptive management, active adaptive management and traditional reductionist scientific investigation. The resultant synthesis of information from this range of sources is likely to be a predictive, robust and credible record of historical change.