Subsurface soil bacterial community composition and the controlling factors remain largely unknown, especially the micro-zone differentiation of community composition within a horizon. We studied a plinthic horizon to determine how different micro-zones in a horizon affect the bacterial community. The plinthic horizon is a net-like horizon characterized by the segregation of iron forms as shown by contrasting red matrix and white veins, which share common macro-environmental conditions such as climate and land use but differ only in physical and chemical compositions. The studied horizon is typical of the red soils of southeastern China and is an important layer in the red soil Critical Zone. The plinthite is considered to have been formed in the Quaternary and thus is a record of the paleo-environment. We evaluated the difference in the bacterial community composition between the red matrix and white veins and explored the possible assembly mechanisms of their co-occurrence patterns. Compared to the eutrophic environments of a red matrix, higher relative abundances of Acidobacteria and Nitrospirae were observed in the white veins. Similarly, more niches led to a higher density of bacterial co-occurrence patterns in the red matrix. The differences in the bacterial community composition and association networks are due to environmental selection, including the legacy of the paleoclimate that is represented by major element contents and contemporary hydrological properties that are mainly controlled by the soil texture. Our study shows that micro-zones even within a same plinthic horizon can provide different habitats and thus select for specific bacterial communities. Furthermore, this study could improve our understanding of the differentiation of bacterial communities among microenvironments caused by both historical and contemporary processes and help to predict how these communities may respond to future environmental changes.