Abstract: In order to study the impact of rice-duck farming ecosystem on zoobenthos biodiversity in paddy waters, surface soil samples taken from rice-duck farming ecosystem and conventional paddy fields were analyzed for zoobenthos biodiversity. The results show that the number of zoobenthos species (genus) declines in rice-duck farming ecosystems compared with conventional paddy. The total number of zoobenthos in riceduck farming ecosystem declines remarkably during the early stage of rice growth, but almost equals that of conventional paddy at late growth stage. Shannon-Wiener diversity index, Simpson diversity index and evenness index all show similar trend of change. The diversity indexes and evenness index of zoobenthos in rice-duck farming ecosystems are higher than those in normal paddy during the early stage of rice growth, but are in the reverse trend during the later stage. The result may have varied implications for water management and implementation of rice-duck farming technology.