<p>Compound-specific isotope analysis of amino acids (CSIA-AA), particularly for nitrogen in muscle tissues of organisms, has been used for identifying the trophic position (TP) of the organisms and the isotope baseline (e.g., the δ values of plants, phytoplankton, etc.) of food webs to illustrate trophic transfer and linkage in ecosystems. However, little is known whether or not other tissues such as scale and blood can be employed as samples for the CSIA-AA. In this study, we compared the tissue-specific δ¹⁵N values of amino acids in several aquatic organisms including fish (e.g., for muscle, scale, blood, bone, etc.), gastropods (i.e., for muscle vs. shell protein), and a turtle (i.e., for yolk vs. embryo) to evaluate applicability of these tissues in the CSIA-AA. The results reveal that the δ¹⁵N values of amino acids in muscle are substantially identical to those in scale, fin, and yolk of fish as well as in shell protein of gastropods, but not to those in internal tissues (e.g., blood, embryo, etc.). Based on these results, we concluded that the former tissues (e.g., scale and shell) are applicable as alternatives to muscle in the CSIA-AA, whereas the latter tissues are not. We suggest that the latter tissues will be required further evaluation when these tissues are employed as samples in the CSIA-AA.</p>