Parent materials and the fertility levels of paddy soils are highly variable in subtropical China.  Bacterial diversity and community composition play pivotal roles in soil ecosystem processes and functions.  However, the effects of parent material and fertility on bacterial diversity and community composition in paddy soils are unclear.  The key soil factors driving the changes in bacterial diversity, community composition, and the specific bacterial species in soils that are derived from different parent materials and have differing fertility levels are unknown.  Soil samples were collected from paddy fields in two areas with different parent materials (quaternary red clay or tertiary sandstone) and two levels of fertility (high or low).  The variations in bacterial diversity indices and communities were evaluated by 454 pyrosequencing which targeted the V4–V5 region of the 16S rRNA gene.  The effects of parent material and fertility on bacterial diversity and community composition were clarified by a two-way ANOVA and a two-way PERMANOVA.  A principal coordinate analysis (PCoA), a redundancy analysis (RDA), and multivariate regression trees (MRT) were used to assess changes in the studied variables and identify the factors affecting bacterial community composition.  Co-occurrence network analysis was performed to find correlations between bacterial genera and specific soil properties, and a statistical analysis of metagenomic profiles (STAMP) was used to determine bacterial genus abundance differences between the soil samples.  The contributions made by parent material and soil fertility to changes in the bacterial diversity indices were comparable, but soil fertility accounted for a larger part of the shift in bacterial community composition than the parent material.  Soil properties, especially soil texture, were strongly associated with bacterial diversity.  The RDA showed that soil organic carbon (SOC) was the primary factor influencing bacterial community composition.  A key threshold for SOC (25.5 g kg^–1) separated low fertility soils from high fertility soils.  The network analysis implied that bacterial interactions tended towards cooperation and that copiotrophic bacteria became dominant when the soil environment improved.  The STAMP revealed that copiotrophic bacteria, such as Massilia and Rhodanobacter, were more abundant in the high fertility soils, while oligotrophic bacteria, such as Anaerolinea, were dominant in low fertility soils.  The results showed that soil texture played a role in bacterial diversity, but nutrients, especially SOC, shaped bacterial community composition in paddy soils with different parent materials and fertility levels.