Summary Ecological communities are assemblages of species that occur together in space and time. Their properties include composition, structure, habitat, distribution, biological interactions and ecosystem functions. The community concept has a central role in conservation planning, and is a key approach for biodiversity conservation above the species level. The relatively recent application of risk assessment and regulatory systems to conservation of ecological communities has highlighted a number of challenges related to intrinsic uncertainties in the definition, diagnosis and assessment of ecological communities. In this review, I aim to elucidate some key conceptual issues essential to the interpretation of communities. Effective description, diagnosis and assessment of communities rests on an understanding of community theory in relation to environmental gradients and ecosystem dynamics. Continuum and discrete models can both contribute to interpretation of communities for conservation. Different sources of uncertainty are inherent in the key properties that characterize communities. Although some of these are reducible, remaining uncertainty must be incorporated into assessments and decision-making processes for conservation. Protocols for assessing extinction risks of communities address rates of decline in distribution, size of distribution and rates of decline in ecological functions. Some protocols assess these factors in a manner that may be inconsistent with equivalent methods for assessing species. Communities may be viewed in a framework that distinguishes thematic, spatial and temporal scales. These scales influence the outcomes of risk assessment, the benefits and limitations of maps and how well communities perform their function in conservation planning. When applied effectively, ecological communities can be powerful tools for delivering cost-effective outcomes for land-use planning and biodiversity conservation.