Background: The BAG (Bcl-2 associated athanogene) family is a multi-functional group of proteins that perform functions ranges from apoptosis to environmental stress tolerance. The BAG proteins are found in yeast, plants and animals. In plants, especially in Arabidopsis thaliana (Arabidopsis), BAG proteins were found to play roles both in abiotic and biotic stresses tolerance including heat, cold, salt, drought, and pathogens. However, the function of Arabidopsis BAG2 remains largely unknown. Whereas BAG6 was found to play important roles in plants response to biotic stresses, it remains unknown whether BAG6 is involved in plants tolerance to abiotic stresses.Results: In this study, we have characterized functions of the Arabidopsis BAG2 and BAG6 genes. Promoter:GUS analysis results show that both BAG2 and BAG6 genes are expressed in various tissues in Arabidopsis thaliana. Expression of both BAG2 and BAG6 genes is induced by salt, mannitol, and heat stress treatments and by the stress-related hormones including ABA, ethylene, and SA, while BAG6 expression is additionally induced by JA. Germination of the bag2 and bag6 single and bag2 bag6 double mutant seeds are less sensitive to ABA than that of the wild type (WT). Both bag2 and bag6 single mutant and bag2 bag6 double mutant show more survival rate than WT in drought treatment but display less survival rate on 45 ℃ heat stress experiment. Consistently, transcription levels of stress-related genes such as RD29A, RD29B and NCED3 are higher in the mutant than that in the WT. Furthermore, these mutants exhibit lower content of reactive oxygen species (ROS) after drought and ABA treatment but higher ROS accumulation after heat treatment than the WT.Conclusion: These results suggest that BAG2 and BAG6 genes are negatively involved in drought stress but play a positive role in heat stress in Arabidopsis.