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This Minireview focuses on the selective isolation methods for the preparation of cellulose nanocrystals (CNCs) and chitin nanocrystals (ChNCs). Various selective preparation strategies with specific preparation conditions and reaction mechanisms are summarized. In particular, these selective reaction routes include controlled acid hydrolysis and selective oxidations at specific positions of cellulose or chitin fibers as well as particular reaction sites of the repeating monosaccharide building blocks of their main chains. These lead t