The mechanisms by which legumes choose their rhizobial partners operate independently from their ability to fix nitrogen. As a result of this naivety, symbiotic nitrogen fixation is often suboptimal. The initial recognition of the bacterial partner and the subsequent signal transduction in the host root utilises components that are functionally conserved between legumes and probably actinorhiza host plants. However, the later steps, which largely determine symbiotic performance, are subject to ongoing evolutionary diversification of molecular mechanisms. For example, the impact of bacterial effector proteins, the occurrence of terminal bacteroid differentiation and the expression of bacterial hydrogenase, all depend on the plant genotype. Strategies towards increased nitrogen fixation of legumes in agriculture need to encompass this diversification of mechanisms.