A certified reference material (CRM) for the analysis of nutrient elements in an edible mushroom (Ganoderma lyceum) powder has been developed (KRISS CRM 108-10-011). The mass fractions of calcium (Ca), iron (Fe), and zinc (Zn) were measured by isotope dilution inductively coupled plasma mass spectrometry (ID ICP/MS). To dissolve the fungi cell wall of mushroom consisted of chitin fibers, sample preparation method by single reaction chamber type microwave-assisted acid digestion with acid mixtures was optimized. The mean measurement results obtained from 12 sample bottles were used to assign as the certified values for the CRM and the between-bottle homogeneities were evaluated from the relative standard deviations. The certified values were metrologically traceable to the definition of the kilogram in the International System of Units (SI). This CRM is expected to be used for validation of analytical methods or quality control of measurement results in analytical lab-oratories when they determine the mass fractions of elements in mushroom or other similar samples.