Transitional environments such as coastal lagoons with narrow connections to the sea are ecosystems very sensitive to natural or anthropogenic pressures. They are biodiversity hotspots and for this reason it should be studied and preserved. This study lists the benthic Foraminifera species from the Saquarema lagoonal system (SLS), Rio de Janeiro state, Brazil. This complex ecosystem consists of four large connected lagoons, namely Urussanga, Jardim, Boqueirão, and Saquarema. A poorly diversified benthic foraminiferal assemblage was documented from most of the lagoon system and consisted of only eight species belonging to three orders and four families. The relatively low species richness of the SLS compared to other Brazilian coastal lagoons might be explained by several factors including domestic sewage input and the long residence time of water.