Among soil disinfestation practices, the application of steam to the soil prior to cultivation is one of the most commonly used management strategies. Growers use steam to effectively kill pathogens by heating the soil. Recently, growers of cut-flowers have noticed a reduction in flower size and weight, which they attribute to steaming the soil. Since shorter and lighter plants lose their commercial value, and therefore, are not accepted in the international market, there is a need to study in more detail the effects of steaming soil on plants and their microbial communities. The overall objective of this study was to determine the effect of consecutive steam application on the rhizosphere soil microbial community of chrysanthemum, and in particular the effects on specific bacterial groups (Pseudomonas spp. and Bacillus spp.). We hypothesized that repeated steam disinfestations cause irreversible changes in the soil community structure, leading to increases of bacterial groups that can be allelopathic for the plant, and that applications of plant growth-promoting rhizobacteria (PGPR) will remediate those effects. To examine the effects of steaming on the rhizosphere microbiota a greenhouse pot assay experiment was conducted using chrysanthemum cultivar golden Kent as a model plant. Rhizosphere soil samples were collected from chrysanthemum plants cultivated in soil that was subjected to steam once, steamed once with PGPR, steamed twice, and not steamed. Our results indicated that repeated steaming of soil changed the abundance of the microbial community, in particular increasing Pseudomonas populations. Although, the characterization of the functional traits of Pseudomonas cultured isolates showed that they produced differential levels of IAA and HCN, steaming the soil did not result in changes in functional traits of the Pseudomonas species compared to isolates from non-steamed soil. Therefore, the magnitude of the effect of soil steaming is related more to the abundance and composition of the pseudomonad community than the functional traits of any individual Pseudomonas species. Additionally, PGPR did not cause changes in the abundance of fluorescent pseudomonads but did have effects on rhizosphere and endophyte colonization. To assess the effect of consecutive steaming on the soil bacterial communities, DGGE, a molecular technique based on the 16S rDNA was used. Results indicated that steaming the soil once does not have a major impact on the soil eubacterial community structure of the rhizosphere, but does impact to some extent the soil microbial community when reapplied. However, potentially important differences in the communities of specific bacterial groups (Pseudomonas and Bacillus) are caused by steaming. There are many ways in which steaming the soil can affect the microbial properties of the soil. We found that steaming the soil increases the abundance of one of the main rhizosphere groups, the fluorescent pseudomonads, and that those changes are related to chrysanthemum growth reduction in the field.