The photosynthetic bacterium Rhodobacter sphaeroides (R. sphaeroides) f. sp. denitrificans IL106 accumulates trehalose as the major organic osmoprotectant in response to a salt stress. An analysis of the R. sphaeroides 2.4.1 genome sequence revealed the presence of five different genes encoding enzymes belonging to three putative trehalose biosynthesis pathways (OtsA-OtsB, TreY-TreZ, and TreS). The function of the different pathways of trehalose was studied by characterizing strains defective in individual trehalose biosynthetic routes. A phenotypic comparison revealed that trehalose synthesis in R. sphaeroides f. sp. denitrificans IL106 is mediated mainly by the OtsA-OtsB pathway and, to some extent, by the TreY-TreZ pathway. Strains with the simultaneous inactivation of these two pathways were completely unable to synthesize trehalose. On the other hand, treS mutants showed an increase in the trehalose level. These results suggest that treS plays a role in trehalose degradation. In addition, treS was found to be important in reducing trehalose after osmotic stress was removed. In this report, we show that the strains that accumulate the most trehalose adapt to salt stress earlier. This is the first report of an organism using multiple pathways to synthesize trehalose solely for use as a compatible solute against salt stress.