A pressing need of algal aquaculture is the availability of strains with favourable characteristics. Since this goal cannot be achieved easily by traditional breeding methods for Gracilaria tenuistipitata, we developed mutagenesis and selection procedures that bypass the necessity for protoplast isolation and cultivation. A haploid gametophyte was identified through chromosome analysis and used for mutagenesis. Chromosomal analyses showed that the haploid plant contains several layers of mononucleated cells at the surface and many large multinucleated syncytiums in the internal region. Chromosomal division of all nuclei in a syncytium was in synchrony. Mononucleated cells were more sensitive to both UV and DNA insertion mutagenesis. UV treatment generated many cadmium (Cd) resistant mutants, but most mutants exhibited retarded growth rate. However, several stable Cd resistant mutants were obtained through reselection. Plasmid pCaMVCAT could be used for DNA insertion mutagenesis in G. tenuistipitata. Stable mutants with increased resistance to chloramphenicol were selected.