In this study, we investigated the effects of a change in growth temperature on the transcriptome of two strains of Pseudomonas aeruginosa. The chosen P. aeruginosa strains were M18 and PAO1, which are adapted to two different niches, rhizosphere and human, respectively. To assess the changes induced by a change in temperature, we used a newly designed microarray covering the complete genome of four P. aeruginosa strains: PAO1, M18, PA14 and LESB58, which proved informative and reliable for the transcriptome study. Using the microarray, we analysed the transcriptome profile changes of two P. aeruginosa strains of M18 and PAO1 at their originating and non-originating temperatures: 28 A degrees C for the rhizosphere and 37 A degrees C for the human. The transcriptome profiles showed significant temperature-dependent differences (64.8 % in M18 and 66.8 % in PAO1) compared with the genome structure (6 % in M18 and 4.1 % in PAO1). Furthermore, we found that the specific induced genes at the non-originating growth temperature of the each strain (207 genes in M18 and 229 genes in PAO1) were evidently more than those induced at the originating growth temperature (158 genes in M18 and 169 genes in PAO1). The functional analysis of several newly found specific regulated operons (such as phh, liu, hmg) in the two strains indicated possible strategies implemented to respond to the non-originating temperature. This study provides new insight into how P. aeruginosa species responds to temperature change and a microarray platform covering the complete genomes of four widely studied P. aeruginosa strains.