<p>The Atlantic Forest presents great biological complexity and high richness and endemism levels, but it is one of the most threatened phytogeographic domain on the planet. Brazil is one of the Rubiaceae diversity centers in the Neotropics. The relevance and representativeness of the Rubiaceae family in the Atlantic Forest is highlighted in floristic composition studies and tropical forest community structures. However, despite the urban expansion in the state of Rio de Janeiro, we still find large areas of continuous vegetation with high connectivity degree. Recently, Rubiaceae flora and floristic surveys were conducted in <em>Restinga</em> and forest areas of Rio de Janeiro state protected by Conservation Units. New Rubiaceae species also have been described in the fluminense flora and they showed localized distributions and small populations. The current paper analyzes the floristic composition of the Rubiaceae in eight Atlantic Forest remnants in the State of Rio de Janeiro - Área de Proteção Ambiental de Grumari, Área de Proteção Ambiental Palmares, Parque Estadual da Serra da Tiririca, Parque Nacional do Itatiaia, Parque Nacional de Jurubatiba, Reserva Biológica de Poço das Antas, Reserva Biológica do Tinguá e Reserva Ecológica de Macaé de Cima - using the PAST software ("<em>Paleontological Statistics</em>") with Sørensen coefficient. Low similarity levels were found due to the habitats’ heterogeneity. <em>Restinga</em> and forest remnants formed distinct groups. The dendrogram showed the formation of three groups, but only Área de Proteção Ambiental de Grumari and Parque Nacional de Jurubatiba (<em>Restinga</em> areas) showed strong bootstrap support (98%). The current study pointed out 19 micro endemic species from the Atlantic Forest, thus conservation strategies were herein discussed. Discrepancies between the Catalogue of Flora of Rio de Janeiro and the Red Book of Brazilian Flora (two of the main reference catalogs of Brazilian flora) have been identified. We also highlight the need for recollecting microendemic species from the Atlantic Forest. We have suggested developing the Red Book of Endangered Species Plant of the State of Rio de Janeiro and launching research projects based on the phylogeographic approach and on conservation biology to faster broadcast information about species that face restricted distribution in the Atlantic Forest.</p>