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A new method was developed for understanding the distribution of chemical species such as mobile-sodium, total-sodium, mobile-chloride, and total-chloride ions in seashell structures. The microwave digestion method was applied for the dissolution of different chemical species of these elements. Several kinds of solutions were used to separate the various species of sodium and chloride ions. Using this method, the distribution of sodium and chloride ions in seashell structures was revealed to differ markedly. Total-sodium ion concentration seemed to be constant in the different layers. Conversely, total-chloride ion concentration was one order of magnitude less than that of total-sodium ion. Mobile-chloride ion concentration also shows that chloride ion is more mobile than sodium ion.The method is effective in measuring the distribution of the elements of seashell structure whilst preventing their contamination from the surroundings and from the reagents used in the procedure. The detection limits were 5 ng g–1 for sodium, and 20 ng g–1 for chloride ion, respectively.