The authors probed Illumina high-throughput sequencing in Hanjiang River to investigate the community structure, distribution and assembly mechanisms of bacterioplankton integrally and rare taxa (RT), abundant taxa (AT) respectively. Hanjiang River bacteria spanned across 22 phyla, 55 classes, 93 orders, 132 families and 164 genera dominated by Proteobacteria, Actinobacteria and Bacteroidetes. 4035 ASVS (80.2%) were defined as RT. Significant seasonal differences were found of the bacteria community by alpha diversity and this pattern were intensified by RT. Non-metric multidimensional scaling (NMDS) showed insignificant differences of the seasonal and spatial distribution of bacteria community in Hanjiang River. Mantel tests considered dissolved oxygen (DO) and ammonia nitrogen as primary influencing factors of autumn microbiome community. Variance partitioning analysis (VPA) indicated more stress from environmental factors to the bacteria community compared with spatial factors. The holistic bacteria community was dominated by deterministic process, while both RT and AT were mainly affected by stochastic process. Overall, RT was mainly influenced by environmental selection as opposed to AT which were more inclined to stochastic distribution.