The present study aimed to examine the effects of applying composted aquatic plants (CAP) on richness and composition of soil bacterial assemblages responsible for alkaline phosphatase production by pot experiments, as compared to the corresponding effects of inorganic chemical fertilizers (ICF). Soil bacterial assemblages were studied by metabarcoding the 16S region of ribosomal DNA as a universal genetic marker and the phoD alkaline phosphatase gene as a functional marker. The compositions of 16S and phoD assemblages were significantly different among soils applied with CAP, ICF, their mixture (MIX), and control (no application). Furthermore, the richness of phoD assemblages in soils was greater in CAP or MIX application than in ICF or control, although significant difference only existed between MIX and ICF. In conclusion, the present study illustrated that the application of composted aquatic plants affected the richness and composition of soil bacterial assemblages responsible for the production of alkaline phosphatase.