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Sediment cores taken from different areas of the mesotrophic Lake Erhai were analysed to investigate the vertical distribution of bacterial community composition (BCC), as well as physicochemical parameters. PCR-denaturing gradient gel electrophoresis (DGGE), stable carbon isotope (δ13C), C/N atomic ratio and canonical correspondence analysis (CCA) were used to explore the relationships between the succession of bacterial communities and environmental variables, emphasising changes in the sources of organic matter (OM). The BCC in natural environments was characterised by DGGE of the 16S rRNA gene with subsequent sequencing of bands of interest. The CCA revealed that the depth-related variation in sediment bacterial communities in different areas of the lake was significantly inﬂuenced by varying environmental factors. The OM source, however, played an important role in structuring BCC at all sites. The DGGE banding patterns revealed that the abundance of Deltaproteobacteria decreased with accompanying elevated levels of C4 plant-derived organic carbon. The sequencing of DGGE bands suggested that the majority of the sequences were affiliated with common phylogenetic groups in lake sediments: Chloroflexi, Deltaproteobacteria and Firmicutes. Betaproteobacteria detected in our study appeared as a prominent phylotype in the upper sediment. The Shannon-Wiener diversity index of bacterial communities was directly affected by the OM source. Constant OM sources resulted in a stable higher diversity of bacterial communities and broader enzymatic capabilities to access OM. We conclude that the differences in the diversity of bacterial communities in sediments differing in their sources of OM were related to environmental variables (e.g. water level, river runoff and terrestrial vegetation composition). Our study provided insights into the relationships between natural BCC and OM sources, facilitating a better understanding of microbial community structure in lake sediment.