The more than 35 described biogenic polyamines have important roles in physiological processes ranging from acid-base buffering to the scavenging of oxygen free radicals. As such they have key cellular- and organismal-level functions in environmental adaptation, cell growth, cell differentiation, fertilization, and biomineralization. To determine cellular polyamine distribution profiles in animals at the base of the phylogenetic tree, the acid-extracted polyamines from cultured cells of a unicellular choanoflagellate and whole bodies of five multicellular invertebrate groups (total 20 species) were quantitatively analyzed using high-performance liquid chromatography and high-performance gas chromatography. Both the choanoflagellate and hydra contained putrescine and spermidine. Diaminopropane, putrescine, cadaverine, norspermidine, spermidine, homospermidine, norspermine, spermine, thermospermine and agmatine were commonly identified among the other invertebrates. In unusual/rare polyamines, aminopropylhomospermidine, homospermine, caldopentamine and homopentamine were found in sponges; aminopropylhomospermidine and canavalmine in the comb jelly; canavalmine, aminopropylcanavalmine and homopyropentamine in jellyfishes; and canavalmine and homopyropentamine in sea anemones. However, long-chain polyamines were not found in soft corals.