Sanya Bay lies at the southern part of Hainan Island, 18°15′N 109°28′E. The seawater in the bay has been catastrophically polluted during the past two decades with urban sewage from the rapidly developing Sanya City. The marine flora research in Sanya Bay was started at the beginning of the 1930s and the most detailed studies were performed by two German-Chinese expeditions in 1990 (October–December) and in 1992 (March–April). In April, October, November and December 2008–2010 the marine flora of Sanya Bay was studied by the authors at three localities: Luhuitou Peninsula, Xiaodong Hai and Dadong Hai. Marine algae were sampled in the intertidal and upper subtidal zones (to 4–5 m depth). The list of species (including varieties and forms) of the marine algae for Sanya Bay sampled during the period from 2008 to 2010 is compared with those collected at the same localities in 1990/1992. Comparative analysis of the floristic composition of the marine red, brown and green algae (found during different time periods) revealed that considerable changes have taken place between 1990/1992 and 2008–2010 at Sanya Bay. There was an increase in filamentous, tubular and fine blade-like green and red algae (mainly epiphytes with a high surface to volume ratio) and a displacement of upright-growing fleshy, foliose and other large green, brown and red algae with a low surface to volume ratio. It is assumed that the changes reflect mainly increased pollution by urban sewage and mariculture pond wastes and probably by coral bleaching events of 1998.