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Abstract Background Limnoperna fortunei is a freshwater bivalve mollusc originally from southern Asia that invaded South America in the 1990’s. Due to its highly efficient water pumping and filtering, and its capacity to form strong adhesions to a variety of substrates by byssus thread, this invasive species has been able to adapt to several environments across South America, causing significant ecological and economic damages. By gaining a deeper understanding of the biological and ecological aspects of L. fortunei we will be able to establish more effective strategies to manage its invasion. The gills of the mollusc are key structures responsible for several biological functions, including respiration and feeding. In this work, we characterized the ultrastructure of L. fortunei gills and its ciliary epithelium using light microscopy, transmission and scanning electron microscopies. This is the first report of the morphology of the epithelial cells and cilia of the gill of L. fortunei visualized in high resolution. Results The analysis showed highly organized and abundant ciliary structures (lateral cilia, laterofrontal cirri and frontal cilia) on the entire length of the branchial epithelium. Mitochondria, smooth endoplasmic reticulum and glycogen granules were abundantly found in the epithelial cells of the gills, demonstrating the energy-demanding function of these structures. Neutral mucopolysaccharides (low viscosity mucus) were observed on the frontal surface of the gill filaments and acid mucopolysaccharides (high viscosity mucus) were observed to be spread out, mainly on the lateral tract. Spherical vesicles, possibly containing mucus, could also be observed in these cells. These findings demonstrate the importance of the mucociliary processes in particle capture and selection. Conclusions Our data suggest that the mechanism used by this mollusc for particle capture and selection could contribute to a better understanding of key aspects of invasion and also in the establishment of more efficient and economically viable strategies of population control.