Trehalose (α-D-glucopyranosyl-1,1-α-D-glucopyranoside) is a non-reducing disaccharide. It is currently thought that just trace level of trehalose was detected in plants, and that trehalose metabolic pathway was significantly related to stress tolerance. In this study, we report that expression levels of three genes with regard to trehalose metabolic pathway were measured in Arabidopsis thaliana, including AtTPS1, AtTPPA and AtTRE1. As a result, transcriptional levels of these genes are the highest in floral organ, and the expression of AtTRE1 is much more than AtTPS1 and AtTPPA. Additionally, we present transcriptional response analyses in drought and heat stresses, which have shown the changes of these genes expression from tolerance in early stress to senescence in later stress.