Macroalgae contains high concentrations of polysaccharides, polyphenols and secondary metabolites. Those compounds are factors that prevent the isolation of deoxyribonucleic acid (DNA) and therefore inhibit the polymerase chain reaction (PCR) that is the beginning for the application of any molecular marker. In the present study, the application of six extraction methods was documented; four of them conventional and two commercial kits. The highest efficiency in DNA extraction was obtained with a conventional method with modifications. Said modifications consisted of immersing the algal tissue in ß-mercantoethanol and the addition of the DIECA salt in the extraction buffer. To test the purity of the DNA, in addition to the electrophoresis and spectrophotometry methods, a PCR was performed for the ISSR molecular marker, obtaining amplified fragments using the aforementioned modification.