Important industrial projects may have a very significant impact on continental and marine biodiversity. In such cases, the authorities have to arbitrate conflicts opposing those who prioritize economic growth, wealth creation, and jobs preservation and those who favor conservation of the natural environment. However, the intricacy of vested interests and the presence of different visions of man-nature relationships and services offered by nature lead to ambiguous attitudes of the decision makers towards biodiversity. In two cases of industrial plants and projects in a big Mediterranean metropolitan area, triggering tough controversies and where biodiversity is at stake, the motives of the private and public parties are examined. By studying comprehensively the arguments of the parties and analyzing the attitudes of the public institutions involved in the cases, we show how the weight placed on biodiversity in the controversies is strongly variable among the different actors, and is often less a reflect of the current state of scientific knowledge than the expression of values and preferences related to the social representations of man-nature interactions and nature's services. We also show the contrasted attention on continental versus marine biodiversity. Further, we show how the territorial divisions in which the institutional tools for dispute resolution are mobilized and the time and space horizons of the actors are poorly related to the spatial and temporal frameworks within which biodiversity and the environment are affected.