A floristic study of marine macrophytic algae and Cyanobacteria in the splash and intertidal zones at Luhuitou reef, Sanya Bay, Hainan Island, China, was conducted during the rainy and dry seasons of 2008−2012 utilizing 148 of the most common species. Macrophytic algal diversity increased from the splash zone to the low intertidal zone, while cyanobacterial diversity decreased. In the upper and middle intertidal zones, the dominant species (primarily highly productive ephemerals) changed frequently throughout each year. In the low intertidal zone, the dominant species (mainly annual fleshy, foliose and coriaceous forms) also changed. In the dry season, species numbers were 33% higher than in the rainy season. During the rainy season, Cyanobacteria dominated the splash zone, while green and red algae dominated in increasing numbers from the upper to the low intertidal zones. During the dry season the splash zone was devoid of all macrophytic algae, and only one species of Cyanobacteria survived. In the upper intertidal, Cyanobacteria and red algae prevailed, while in the mid and low zones, red and green algae were the most diverse. In spite of heavy pollution in Sanya Bay, there was no evidence of dramatic changes in species numbers or composition, and the marine flora was similar to that of unpolluted regions in the Indo-Pacific.