Standard procedures for isolating nucleic acids from specialized tissues such as the mucus-containing tissues found in many marine organisms are, in many cases, not effective, resulting in isolates contaminated with polysaccharides that encumber subsequent analysis. A method is described for isolating nucleic acids from the sea anemone Condylactis gigantea (Cnidaria: Anthozoa) using the compound hexadecyltrimethyl ammonium bromide (CTAB). This substance has historically been effective in producing digestible chromosomal DNA from a variety of polysaccharide-enriched sources. In the presence of CTAB, DNA can be isolated and extracted from Condylactis gigantea and is suitable for digestion with restriction endonucleases. With a minor modification, RNA can also be extracted and used to obtain mRNA. The technique is useful for Cnidarian tissues and may be appropriate for a variety of other marine invertebrates and algae.