We have purified and characterized a deoxyribonuclease from zygotes of the eukaryotic green alga, Chlamydomonas reinhardtii and investigated effects of the polyamines, putrescine, spermidine and spermine on the purifed endonuclease-catalyzed cleavage of plasmid DNA. The enzyme has a molecular weight of about 37 kDa as measured by gel filtration and SDS-polyacrylamide gel electrophoresis. There is no requirement for a divalent cation. The activity is sensitive to ionic strength, as NaCl and KCl result in inhibition. The cleavage of plasmid DNA by the purified endonuclease was effectively inhibited by polyamines. The enzyme activity was inhibited more effectively by spermine than by spermidine. The inhibition by putrescine was lower than the other two polyamines.