Resting cysts play a major role in the life history of dinoflagellates. Peridiniopsis blooms have occurred many times in the Jiulongjiang River (Fujian province) since February 2009. This study investigates the characteristics of dinoflagellate cysts found in the sediments of the Xipi Reservoir in the Jiulongjiang River during different months, from 2012 to 2013. We used microscopy and single-cell Polymerase Chain Reaction (PCR) technology to identify the species of dinoflagellate cysts in a germination experiment. The results show that Peridiniopsis forms the dominant genus among the dinoflagellate cysts found in these sediments, and accounts for 80% of the total population while the rest belong to the genus Gymnodinium. We identified the cysts of Peridiniopsis penardii, the dominant bloom species in 2009. We also assessed the distribution and abundance of dinoflagellate cysts and investigated the driving factors of these population characteristics. The abundances of dinoflagellate cysts in sediments during different months are between (13.7 ± 1.2) to (105.2 ± 8.3) cysts/g DW. The multiple correlation analysis demonstrated that the abundance of dinoflagellate cysts is significantly positively correlated with moisture (P < 0.05). It showed that the distribution of dinoflagellate cysts gradually increased along the direction of the river flow. These results provide new insight into freshwater dinoflagellate cyst characterization and germination in this reservoir, and provide a scientific background for efforts aimed at the prevention of dinoflagellate blooms in the Jiulongjiang River.