For clear observation of diatom frustules, both inner- and extracellular impurities need to be eliminated from samples. This process is usually performed using oxidizing acids that can completely decompose organic matter. However, oxidizing acids often result in dissociation of frustules, and if oxidative byproducts are not washed out completely at the end of the process, they can act as impurities. Moreover, the treatment is time-consuming, and the necessity for subsequent rinsing may reduce the number of diatom frustules and/or valves because of loss during rinsing. Application of low-temperature plasma (LTP) was examined for diatom cleaning. LTP treatment is an extremely gentle cleaning method in which all the processes can be performed on a cover slip without rinsing with distilled water or the addition of chemicals. Application of this method to the tidal flat sample was found to be effective for the preservation of complete frustules, such as those observed in Amphora, Cocconeis and Planothidium species; with this treatment, there was no reduction in the diatom population during the cleaning process.