The protection of biodiversity is a complex societal, political and ultimately practical imperative of current global society. The imperative builds upon scientific knowledge on human dependence on the life-support systems of the Earth. This paper aims at introducing main types of uncertainty inherent in biodiversity science, policy and management, as an introduction to a companion paper summarizing practical experiences of scientists and scholars (Haila et al. 2014). Uncertainty is a cluster concept: the actual nature of uncertainty is inherently context-bound. We use semantic space as a conceptual device to identify key dimensions of uncertainty in the context of biodiversity protection; these relate to [i] data; [ii] proxies; [iii] concepts; [iv] policy and management; and [v] normative goals. Semantic space offers an analytic perspective for drawing critical distinctions between types of uncertainty, identifying fruitful resonances that help to cope with the uncertainties, and building up collaboration between different specialists to support mutual social learning.