An inventory of macrophytic algae on the Con Dao Islands (Vietnam) in the South China Sea (8°38′ N, 106°41′ E) was carried out for the first time by Vietnamese and Russian phycologists from 1986 to 2008. Algae were collected in different years of this period. The first collections of marine algae from the Con Dao Islands were obtained in 1986 in the framework of the Soviet–Vietnamese expedition aboard the R/V Akademik Nesmeyanov. The following samplings were conducted during the expedition of the Institute of Marine Environment and Resources, Vietnamese Academy of Science and Technology, in March and April 1996. In 2003, marine algae were collected around Con Son Island by Vietnamese and Japanese phycologists. In 2008, marine algae were collected along the coast of Con Son Island by the authors of the present article. In all collections (1986–2008), a total of 201 species of algae were found on the Con Dao Islands, of which 54% were red, 18% were brown, and 28% were green algae. A comparison of the collections sampled in 1986–2008 has shown significant changes in species composition of the marine flora during the period: in each taxonomic group of macrophytes, there was a proportional replacement of some species by others. It is suggested that the revealed decadal changes in the flora do not depend on climatic or anthropogenic changes in the environment, but these changes are natural, possibly periodic, fluctuations in the population density of individual algal species, regulated by internal factors of the ecosystem.