An invasive alien weed, Ageratina adenophora, has become widespread in the southwest of China due to its high environmental adaptation. In the present study, in order to understand the molecular aspects of resistance to heat and cold stress, we investigated the characterization and expression of heat shock protein genes (designated as Aahsp70 and Aahsp90) in A. adenophora. The cDNA of A. adenophora Aahsp70 and Aahsp90 was cloned by the combination of homology cloning and rapid amplification of cDNA ends (RACE). The Basic Local Alignment Search Tool analyses revealed that Aahsp70 and Aahsp90 shared high levels of identity with corresponding proteins from other species. Hybridization was employed to examine the expression patterns of Aahsp70 and Aahsp90. The relative expression levels of the Aahsp70 and Aahsp90 transcripts were both up-regulated and reached maximal levels at 2-4 h after heat shock. Then, Aahsp70 dropped progressively to the original level at ~4 h after heat shock. The transcriptional changes of Aahsp70 and Aahsp90 both were more obvious under cold stress. Recombinant Aahsp70 and Aahsp90 improved the viability, in comparison with the control cultures, of Escherichia coli under stress conditions. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the cell lysates suggested that the protective effect in vivo was related to increased thermo-stability of the soluble cytosolic proteins. This study emphasizes that the relationship between, and regulation of, heat shock proteins might incorporate variable strengths to increase the adaptation of A. adenophora.