According to traditional biogeographic theory, historical contingency can influence soil microbial communities. Thus, we ask: are historical contingencies (soil profiles and geographic sampling locations), or other factors (seasonal changes and soil nutrients), important drivers of soil bacterial communities? This study used high throughput sequencing technology to investigate the soil bacterial compositions of rubber plantations at the local and geographic scales. Significant differences were detected in bacterial compositions between two study locations, Xishuangbanna and Hainan Island. Redundancy analysis showed that the most important factor driving bacterial composition was site location and total nitrogen, which explained 38.2 and 38.4% the total variance, respectively; this indicates that historical contingencies drive distinct bacterial communities in rubber plantation soils. At the local scale, there were also distinct differences in soil bacterial compositions between the dry and rainy season in both the Xishuangbanna and Hainan sites. Seasonal changes explained 13.6 and 41.4% of the total variation of soil bacterial composition in Xishuangbanna and on Hainan Island, respectively, whereas other factors had little effect on soil bacterial communities (p < 0.001). In conclusion, our results demonstrate that historical contingencies drive variation in bacterial composition at the geographic scale, whereas seasonal changes influence variation at the local scale.