Compared with studies on the effects of transgenic food crops, those on the effects of transgenic ornamental plants on soil microbial communities are limited. We investigated the potential effects of transgenic dwarf chrysanthemum, containing the short internode related sequence 7 (SRS7) gene from Chinese cabbage, on the relative abundance and composition of the rhizosphere bacterial communities at different plant growth stages (shoot development, flowering, and senescence) using next-generation sequencing. Non-metric multidimensional scaling ordination, permutational multivariate analysis of variance, analysis of similarities, canonical analysis of principal coordinates, and cluster analysis revealed a clear discrimination between bacterial community structures of rhizospheres from all chrysanthemum lines and bulk soil at all growth stages. No differences were observed between soil bacterial communities of the rhizospheres associated with the non-transgenic Peace Copper and transgenic line P-13. However, soil bacterial community structures of rhizospheres associated with Peace Copper and transgenic line P-33 showed a clear distinction at the shoot development stage. This might be attributed to the lower growth rates of P-33 than those of Peace Copper; however, this difference was temporal and diminished at the flowering and senescence stages. Our results suggest that the cultivation of these transgenic chrysanthemum lines is not likely to alter the bacterial communities in the rhizosphere.