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The use of systematic conservation planning to establish conservation priorities will not necessarily attract sufficient public and policy support if the process does not explicitly consider public preferences. The Southwest Australia Ecoregion Initiative presented an opportunity to examine whether an expert-driven, systematic conservation planning process was likely to reflect public preferences for biodiversity conservation. Specifically, a discrete choice experiment was administered to both scientists and the public to generate non-market values for protecting a set of key conservation features, relevant to the planning exercise. The study demonstrates that conservation preferences differ between scientists and the public. With this finding in mind, a novel approach is outlined for incorporating non-market values - derived from a choice experiment - into a systematic conservation planning framework.