This paper originates from an address at the 8th International Symposium on Nitrogen Fixation with Non-Legumes, Sydney, NSW, December 2000 We examined growth responses of rice seedlings (Oryza sativaL. cv. Pelde) to specific Rhizobium strains and their mutants, to investigate the molecular basis of colonization and the stimulation or inhibition of rice growth and development by rhizobia. Inoculation experiments with rice seedlings showed that specific Rhizobium isolates of these rice-associated and legume-associated rhizobia could either promote, inhibit, or have no influence on rice plant growth. There are genes on certain plasmids of Rhizobium leguminosarum bv. trifolii and R. leguminosarum bv. viciae that affect the growth and development of rice root morphology. Additionally, we found that bacteria can intimately associate with, and enter into, rice seedling roots by alternative mechanisms to those encoded by the symbiotic (pSym) and the tumour-inducing (Ti) plasmids. Investigations suggest an involvement of the phytohormone auxin, and possibly nitrate, in this complex rice–Rhizobium interaction.