Two Lotus species, L. japonicus and L. pedunculatus (uliginosus), show opposite nodule phenotypes when inoculated with rhizobial strains Mesorhizobium loti NZP2235 and Bradyrhizobium NZP2309. NZP2235 is inducing pink, nitrogen fixing nodules, when applied to Lotus japonicus, while Lotus pedunculatus infected with the same strain of rhizobia, is producing white uninfected nodules. On the other hand the slow-growing NZP2309 induces functional nodules on Lotus pedunculatus, whereas the nodules induced on Lotus japonicus are infected, but without the ability to supply the plant with nitrogen. The phenotypes are characterized in detail using thin-section microscopy of the nodules, and acetylene reduction assays. Infection threads are visualized by lacZ staining of bacteria, and using rhizobia that carries an eGFP marker-gene. Last but not least, to investigate the phenotype at a molecular level, the expression levels of 6 nodulins are analysed, in functional nodules (L.japonicus NZP2235) and non-functional nodules (L.japonicus NZP2309).