Zhanjiang is located in the South China Sea and is rich in seaweed resources, but studies on the species diversity of the genus Gracilaria are scarce. To clarify the diversity of Gracilaria species and their phylogenetic relationships in this region, this study was conducted to taxonomically investigate the intertidal macroalgae resources in Zhanjiang waters through morphological, anatomical and molecular analyses. The results showed that five species were identified, namely Gracilaria hainanensis, G. salicornia, G. spinulosa, and two undescribed species (Gracilaria sp.). The taxonomic status of these five Gracilaria species is discussed in detail, and detailed and rich anatomical characterization images and molecular sequence data are provided. This study not only enriches the diversity of Gracilaria species in the Zhanjiang Sea, but also provides a scientific basis for the development of seaweed resources and biodiversity conservation in the region.