Trehalases are enzymes that carry out the degradation of the non-reducing disaccharide trehalose. Trehalase phylogeny unveiled three major branches comprising those from bacteria; plant and animals; and those from fungal origin. Comparative analysis between several deduced trehalase structures and the crystallographic structure of bacterial trehalase indicated that these enzyme's structures are highly conserved in spite of the marked differences found at the sequence level. These results suggest a bacterial origin for the trehalases in contrast to an eukaryotic origin, as previously proposed. Trehalases structural analysis showed that they contain six discrete motifs which are characteristic of each phylogenetic group, suggesting a positive evolutionary selection pressure for the structural conservation. Interestingly, trehalases are involved in multiple regulatory functions: In the response against pathogens (plant-pathogen interactions); the regulation of bacterial viability in symbiotic interactions (legume-Rhizobium); carbon partitioning in plants; regulating chitin biosynthesis, as well as energy supply in the hemolymph for flight, in insects. In summary, trehalases seem to have a prokaryotic origin and play an active role in carbon metabolism and other diverse regulatory effects on cell physiology.