A new bacterial secondary messenger, bis-(3',5')-cyclic dimeric guanosine monophosphate (c-di-GMP), is usually synthesized or decomposed by proteins containing GGDEF or glutamate-alanine-leucine (EAL) domain. They often act as cyclase or phosphodiesterase of c-di-GMP and their genes are distributed among almost all bacteria according to known genomic DNA sequences. However, the systematic identification of GGDEF and EAL genes remains unclear in rhizobia, soil bacteria that interact with compatible legumes to form nitrogen-fixing nodules. In this study, 19 putative GGDEF and EAL genes were identified in a model rhizobium, Sinorhizobium meliloti, by bioinformatic analysis (encoding 5 GGDEF proteins, 4 EAL proteins, and 10 GGDEF and EAL double-domain proteins). Null mutants of 14 genes were constructed through systematic plasmid insertion. All 14 gene mutants showed deficient growth in minimal medium and defective motility, and 11 gene mutants produced a lot more exopolysaccharide and displayed less competitive nodulation on the host plant, alfalfa. Our results suggested that GGDEF and EAL proteins may play different roles in the control of S. meliloti physiology, although they contain conserved catalytic (GGDEF or EAL) domains. Our finding also implied that c-di-GMP may play an important role in the interactions between this rhizobium and its host plants to establish efficient symbiosis.