Microcystins have a common structural framework of D-Ala-X--Z-Adda-D-γ-Glu-, where X and Z are variable amino acids; the systematic name "microcystin-XZ" (MC-XZ in short) is then assigned based on the one letter codes (if available; longer codes otherwise) of the amino acids. If the molecule show any other modification, the differences are noted in square brackets before "MC". Of these, several are uncommon non-proteinogenic amino acids:
* D-Masp is D-erythro-β-methyl-isoaspartic acid, a derivative of aspartic acid in β-amino acid form;
* Adda is (all-S,all-E)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid, a β-amino acid exclusively found in microcystin and the related nodularin;
* Mdha is N-methyldehydroalanine, a derivative of dehydroalanine. In nodularin it is replaced by Mdhb (N-methyldehydrobutyrine), another dehydroamino acid derivative.