Macroalgae are key and engineering species on rocky shores worldwide, which support diverse and abundant microbiota with functions of biochemical cycling, host health and development. Meanwhile, the microbiota on the surfaces of macroalgal rocky substrate also plays an important role in marine ecosystem. However, the differences in the epiphytic microbial communities on macroalgae and rocky substrate are still poorly understood. In this study, the epiphytic microbial communities on four macroalgae (Corallina officinalis, Rhodomela confervoides, Sargassum thunbergii, and Ulva linza) and their rocky substrates from Weihai coast zone were characterized using high-throughput sequencing technology.