Cells from Acetabularia mediterranea and Batophora oerstedii have been cloned and several lines established from these clones. Chloroplast DNA (cpDNA) was isolated from these lines and characterized by restriction enzyme analysis. A high degree of restriction fragment length polymorphism was observed between the different lines of each species. This high intraspecific variability in the cpDNA arrangement was confirmed by hybridization to well-characterized chloroplast genes. Based on results obtained from DNA-denaturing experiments, a GC content of 49.9% and 51.7% was calculated for different lines of A. mediterranea and B. oerstedii, respectively. This is close to that found in the cyanobacteria.