Experimental investigations of the relationship between biodiversity and ecosystem functioning (BEF) directly manipulate diversity then monitor ecosystem response to the manipulation. While these studies have generally confirmed the importance of biodiversity to the functioning of ecosystems, their broader significance has been difficult to interpret. The main reasons for this difficulty concern the small scales of the experiment, a bias towards plants and grasslands, and most importantly a general lack of clarity in terms of what attributes of functional diversity (FD) were actually manipulated. We review how functional traits, functional groups, and the relationship between functional and taxonomic diversity have been used in current BEF research. Several points emerged from our review. First, it is critical to distinguish between response and effect functional traits when quantifying or manipulating FD. Second, although it is widely done, using trophic position as a functional group designator does not fit the effect-response trait division needed in BEF research. Third, determining a general relationship between taxonomic and FD is neither necessary nor desirable in BEF research. Fourth, fundamental principles in community and biogeographical ecology that have been largely ignored in BEF research could serve to dramatically improve the scope and predictive capabilities of BEF research. We suggest that distinguishing between functional response traits and functional effect traits both in combinatorial manipulations of biodiversity and in descriptive studies of BEF could markedly improve the power of such studies. We construct a possible framework for predictive, broad-scale BEF research that requires integrating functional, community, biogeographical, and ecosystem ecology with taxonomy.