ABSTRACTIn all seven genera belonging to the order Siphonocladales and in two genera of the Cladophorales (Chlorophyta) that were examined, extracts of total DNA contained abundant low molecular weight (LMW) molecules. This DNA typically ranged in size from 1.5 to 3.0 kb among the different genera studied. The complexity of the populations of molecules found in different genera also varied with regard to sizes and numbers of bands evident in electrophoresis gels. Our data suggest that the LMW DNA is ubiquitous among these algae since it occurred in each of our six isolates of Ernodesmis verticillata (Kützing) Børgesen collected in both the Caribbean and the Gulf of California. The LMW DNA from Ernodesmis and Ventricaria ventricosa (J. Agardh) Olsen et J. West was denser than high molecular weight (HMW) DNA in CsCl/bisbenzimide gradients. Ultrastructurally, the LMW DNA molecules were linear, averaging 0.65 μm (Ernodesmis) and 1.0 μm (Ventricaria) in length. Approximately 2%–5% of the former possessed an apparent loop or lariat at one end, as visualized in the electron microscope after rotary shadowing. The LMW DNA molecules appeared to be predominantly double‐stranded DNA based upon staining with acridine orange. The 2.2‐kb DNA from Ernodesmis has features typical of plasmids in that it rapidly reannealed after heat denaturation, and it was selectively enriched in an alkaline‐lysis extraction procedure. In denaturing gels, this DNA migrated at >4.0 kb, indicating that the molecules may actually be single‐stranded DNA species with intramolecular base pairing, each containing a long inverted repeat folded back on itself in a hairpin conformation in the native state. Digestion with mung bean nuclease revealed that additional single‐stranded regions may occur in many of the LMW molecules, in addition to the hairpin loop. Although the endonuclease DNase I rapidly digested the LMW DNA, neither exonuclease III nor lambda exonuclease digested it. This suggests that the ends of these DNA molecules are protected. Collectively, the data indicate that members of the Siphonocladales and Cladophorales contain linear plasmid‐like DNA molecules that appear to have a novel combination of features.