Ecological concepts and data may justify the selection of biodiversity conservation plans among different options, but can also lead to poor conservation guidelines if not properly used. The use and meaning of the 'surrogate' concept in ecology and conservation planning contexts is a typical example. Surrogates are entities such as species, environmental variables or habitats, which are used to represent a target entity such as genes, species, ecosystems or related metrics. 'Pattern-based surrogacy' identifies effective surrogates using statistical congruence, while 'selection-based surrogacy' identifies effective surrogates through a notional conservation plan or prioritization analysis where sites are added to a set of protected areas, often using a complementarity criterion between sites. With this clear framework in mind, an investigation of the coral reef literature revealed that most published studies on surrogates of reef biodiversity refer in fact to pattern-based surrogates. Fundamentally, there is nothing wrong with both approaches. However, efficient pattern-based surrogates are often recommended for conservation planning, implying that they could be efficient selection-based surrogates. In fact, efficient pattern-based surrogates are not necessarily efficient selection-based surrogates and vice versa. The reason is the complementarity rules used by selection algorithms. We call for more clarity from authors on the context in which effective surrogates have to be used, and more caution from managers when surrogates are to be used in conservation plans.