Epiphytism is a common phenomenon in seaweeds that can be observed in natural populations and under culture conditions. Epiphytes are generally attached superficially to the surface of the host. Some epiphytic species can penetrate into the tissue of the host, affecting its growth and productivity. This study was done to examine epiphytism in three Gracilaria species: G. fisheri, G. salicornia, and G. tenuistipitata. Sampling of natural and cultured populations was conducted at seven sites. The samples were examined using a light microscope (LM) and scanning electron microscope (SEM). In this study, the epiphytic algae found were mainly cyanobacteria (Lyngbya), Chlorophyceae (Cladophora and Ulva), Phaeophyceae (Padina), and Rhodophyceae (Ceramium, Hypnea, and Polysiphonia). Lyngbya majuscula had the highest density in G. fisheri (14.56 epiphytes cm−2; 40% host−1). A high density of Polysiphonia scopulorum (1.16 epiphytes cm−2; 30% host−1) was found on the G. fisheri plants. In addition, Cladophora species were found on all the Gracilaria species, particularly on G. salicornia plants (4.04 epiphytes cm−2; 43.33% host−1). G. salicornia plants were frequently dominated by Hypnea hamulosa (2.94 epiphytes cm−2; 40% host−1). In contrast, a small number of epiphytes were found on G. tenuistipitata compared with the other two species. The SEM micrographs revealed epiphytic attachment to the host and the extent that epiphytes penetrated the host tissues. Our study showed that G. fisheri and G. salicornia had a greater degree of susceptibility to epiphytes than G. tenuistipitata.