| Summary: | The influence of <i>Alternanthera philoxeroide</i> (alligator weed) invasion on wetland organic matter (OM) accumulation and bacterial changes is rarely studied, but is possibly an important step for revealing the invasion mechanism. Thus, the distribution characteristics of light fraction organic carbon and nitrogen (LFOC and LFON), and heavy fractions organic carbon and nitrogen (HFOC and HFON) were analyzed. Sampling was done on two sediment depths (0–15 cm and 15–25 cm) of invaded and normal habitats of two natural wetlands and two constructed wetlands, and bacterial taxa and composition in surface sediments were also analyzed by high-throughput sequencing. In the surface sediments, the LFOC and LFON contents were significantly higher in the constructed wetlands (0.791 and 0.043 g·kg<sup>−1</sup>) than in the natural wetlands (0.500 and 0.022 g·kg<sup>−1</sup>), and the contents of the C and N fractions were also prominently higher in the invaded areas than in normal wetland habitats. The OM storage was relatively stable. Proteobacteria (55.94%), Bacteroidetes (5.74%), Acidobacteria (6.66%), and Chloroflexi (4.67%) were the dominant bacterial phyla in the wetlands. The abundance of Acidobacteria, Actinobacteria, and Gemmatimonadetes were significantly higher in the invaded areas than in the normal habitats. The relative high abundance-based coverage estimator (ACE) index in the constructed wetlands and invaded areas suggested the corresponding high bacterial diversity. The significant and positive relationship between Acidobacteria and organic nitrogen concentrations suggested their potential and positive interrelationships. This study demonstrated that the alligator weed invasion could significantly change the compositions of sediment organic matterand bacteria, thus further changing the nutrition cycle and wetland microhabitat.
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