Freshwater cyanobacteria produce lethal toxins such as microcystins and anatoxins. During the purification of microcystins in bloom samples we found that a toxic cyanobacterium produced not only microcystins but also other types-peptides in early 1990. Since then we have isolated approximately thirty peptides from freshwater cyanobacteria. In this manuscript we focused on the following topics concerning the isolated peptides: 1) how to isolate desired compounds and to determine their structures, 2) structural classification of isolated compounds, 3) isolation of similar peptides from laboratory strains and bloom materials, 4) structurally related peptides from freshwater and marine origins, 5) β-amino acid containing peptides from cyanobacteria, 6) comprehensive analysis system for the biosynthetic study of peptides produced by cyanobacteria, 7) biological activities of isolated compounds.