The chromosomes of Crustacea, especially decapods, are usually numerous, small in size, and punctiform. These characteristics make it difficult for researchers to further investigate the chromosomes by light microscopy. As an alternative, the scanning electron microscopy (SEM) is recommended because it has higher resolution and is able to provide valuable three-dimensional data and X-ray microanalysis. The aim of this study is to obtain some fundamental knowledge for the preparation of the chromosomes of crustaceans for SEM observations. Since crustacean chromosomes are so small, impurities such as mucus and cytoplasm easily obscure the chromosome surface making it impossible for researchers to observe their fine structure. We used Artemia parthenogenetica as a model and confirmed impurities originating from the nauplii paste and the cytoplasm of the cells, and demonstrate that the nauplii paste can be removed by rinsing and the cytoplasm can be digested by trypsin.