This study presents a qualitative analysis of endangered species occurrences in conservation units of Rio de Janeiro, one of the largest Brazilian municipalities in population size. Increasing human activities trigger changes in biodiversity, promote fragmentation, and reduce species distribution ranges, which can ultimately lead to declines in population sizes. One of the main goals of protected areas (PAs), such as conservation units, is to protect and conserve biodiversity. Here, we compiled all vascular plant species recorded within Rio de Janeiro PAs by consulting the Reference Center for Environmental Information (SpeciesLink), Flora do Brasil (2020), and primary data records contained in management plans. We compared this compilation with the list of Brazilian endangered plant species, verifying whether the management plans presented specific programs for these species. Of the 60 surveyed PAs, 24 had records of endangered species and only 17 had management plans, 14 of which had a specific program that contemplated the monitoring and/or conservation of endangered species. A total of 70 endangered species were recorded. The highest numbers of endangered species were found in the Tijuca National Park (41) and the Pedra Branca State Park (17), the two largest PAs with the two largest forest fragments. Despite the high number of endangered species and the number of protected areas that harbor them, few internal programs address endangered species conservation and management. Thus, efforts to maintain endangered species in protected areas can be aided by field data collections that confirm their occurrence and maintenance in these PAs.