Filamentous algae, represented by Spirogyra and Cladophora, exist widely in various natural and aquatic waters, and their overgrowth poses a threat to aquatic environment and cultured animals. In order to explore the key factors for filamentous algae occurrence, five pairs of ponds with and without filamentous algae in the same environment and belonging to the same farmers were selected for this study. Their water quality, bioavailable nitrogen and phosphorus in sediment, as well as filamentous algae propagules were detected and analyzed. The results showed that there were no significant differences in total nitrogen and phosphorus levels between ponds with and without filamentous algae (P>0.05), whereas the content of Chlorophyll a in four ponds in with filamentous algae was significantly higher than that in corresponding ponds without filamentous (P<0.05). The average bioavailable nitrogen content in the sediment of ponds with filamentous algae was (15.72±3.60) mg/kg, whereas the average bioavailable nitrogen content in those without filamentous algae was (13.22±1.97) mg/kg, 2.50 mg/kg lower than that of the former. The average available phosphorus content in the sediment of ponds with filamentous algae was (72.26±10.57) mg/kg, and that of ponds without filamentous algae was (50.33±12.62) mg/kg, 21.93 mg/kg lower than that of the former. The ratio of available N/P in sediment was below 0.5 in the five pairs, and the ratio of available N/P in ponds without filamentous algae was 26.32% higher than that in ponds with filamentous algae. Phytoplankton growth could be inhibited in low N/P ratio condition, whereas filamentous algae has strong adaptability to low nitrogen content and N/P ratio environment. Therefore, at the beginning of culturing, the conditions of low nitrogen content and low N/P ratio in the sediment put the phytoplankton at a disadvantage in the initial niche competition with filamentous algae, and even if the OTUs number of phytoplankton detected was larger than that of filamentous algae propagules, it did not make it the dominant species under the above conditions. In addition, the detection of filamentous algae propagules showed that they were widely present in water bodies and sediment of ponds with and without filamentous algae , as well as in water sources, and filamentous algae propagules were detected even in sterilized and sun-exposed ponds. However, the number of filamentous algae propagants could be reduced by sterilizing and sun-exposing ponds. Therefore, quicklime or bleaching powder alone cannot completely eliminate the occurrence of filamentous algae, but can be used as an auxiliary control measure, whereas controling the interspecific niche competition with the regulation of bioavailable nitrogen content and the ratio of nitrogen and phosphorus is a promising direction of controlling filamentous algae worth further study. The results of this experimental study have important reference value for the research and production practice of filamentous algae prevention and control in aquaculture ponds.