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This study aims to evaluate the diversity of rotifers in various freshwater habitats in Da Nang City, Vietnam, and to investigate the relationship between community structure and environmental conditions. A total of 75 rotifer species belonging to 25 genera and 17 families were recorded, out of which seven species are new to Vietnam. Species from the families Brachionidae and Lecanidae are abundant (containing about 50% and 69.44%, respectively) in the total rotifer species in both lacustrine and riverine habitats. The number of rotifers recorded in the lakes (64 taxa) was much higher than those in rivers (36 taxa), and this is possibly due to the conditions in lakes being more favorable for the development of small zooplanktons. The significant influences of environmental factors (temperature, pH, turbidity, and trophic state) on the rotifer community were well-reflected in the distribution of commonly found species in lakes (p-value < 0.05). Our study results enrich the data on the diversity and the ecology of rotifers in Vietnam.