Multiple biodiversity objectives have been proposed in conservation planning and economics for the Noah’s Ark problem – the problem of allocating limited funds to conservation projects – including species richness, persistence, taxonomic diversity, representativeness, the charismatic value of species, the broader concept of direct utility and ecological importance. However, these objectives are incommensurable and there is little consensus about which objective should be pursued, given the current state of nature. In economics, this is perhaps because the commensurability problem can be solved by converting all biodiversity objectives to monetary values. Yet, even here, a commensurability problem exists because fundamental uncertainty about species interactions means that ecological values cannot be represented in economic terms. Thus, maximising biodiversity value, combined as it is with a rational decision-making framework and assumed known probabilities of survival, can undermine the very values being pursued. This is especially the case when climate change is a current and future state of nature. Climate change adds additional complexity and fundamental uncertainties to the survival probabilities, the future value of species, the interactions among species and the probability of success of conservation projects. The associated incomplete information can lead decision makers to risky decisions under the current approach. Instead, under such conditions, the precautionary principle is appropriate. This leads to a broad conservation strategy of minimising the maximum regret and, when applied to the Noah’s Ark problem, an objective of ecosystem resilience or functional diversity rather than an objective based on economic values. The paper therefore provides an economic justification for focussing conservation resources and threatened species legislation on the resilience of ecosystems.