Abstract: Cylindrospermopsis raciborskii is a species of tropical cyanobacterial that can be found in natural water bodies. It has both toxic and non-toxic, and the coexistence of these genotypes is common. The production of cylindrospermopsin (CYN) is a significant concern due to its high toxicity to humans, and thus investigation on the distribution its toxic strain and the potential affecting factors will help to reduce the toxic risk of C. raciborskii blooms. Based on two surveys (2018 and 2022) in 20 reservoirs in Zhuhai City in tropical southern China, we tried to understand the occurrence of toxic C. raciborskii and assess the health risk of CYN. During the two investigated periods, C. raciborskii and its toxic genotype were detected in all 40 samples by using rpoC1-based qPCR analysis and in 33 samples with cyrJ-based qPCR. The ratios of toxic genotype accounted for 0.046%—38.66% of the total C. raciborskii abundances, indicating that toxic C. raciborskii was widely distributed in Zhuhai reservoirs but had low dominance in the C. raciborskii population. Compared with the year 2018, the averaged abundance of C. raciborskii in the 20 reservoirs increased nearly 10 times in 2022, however there was no significant difference in abundances between the two years. There was a significant reduction in the ratio of toxin-producing genotypes in the population. Both the mean and maximum ratios decreased in 2022 compared to 2018, with the mean ratio declining from 14.86% to 4.17%, and the maximum ratio decreasing from 38.66% to 17.24%. The concentrations of CYN changed with a similar decreasing pattern, with the mean concentration reducing from 0.56 to 0.19 μg/L. Mixed Effect Model showed that elevated PO₄-P and decreased NO₃-N may favor the growth of non-toxic C. raciborskii, and the ratios of toxic C. raciborskii increased with water temperature.