<p>Genetic diversity is essential to the survival and resilience of all species, yet very few studies characterizing the intraspecific genetic diversity of rare species have been carried out. In this study, we assessed and described the genetic diversity and structure of two rare and endemic <i>Myrceugenia</i> species (Myrtaceae) from the Brazilian Atlantic Forest using microsatellite markers developed specifically for each species. We also followed the IUCN guidelines to assess their conservation status and discussed conservation strategies for these species. Our results suggested a moderate level of genetic diversity for both species. <i>Myrceugenia basicordata</i>, distributed at lower altitudes, is the species with the lowest genetic diversity, although with low differentiation among populations. <i>Myrceugenia joinvillensis</i> presented higher genetic diversity and a more distinct genetic structure, possibly because of its exclusive occurrence at higher altitudes. Both species require conservation efforts to avoid future declines in population size and distribution range. The main threat to these species is habitat loss or fragmentation due to urban expansion. Considering this, our practical recommendations for conserving these species include immediate actions, such as including the species in official red lists, and long-term actions, such as <i>ex situ</i> cultivation for future reintroduction. This study represents the first conservation effort focused on <i>Myrceugenia</i> species from the Atlantic Forest, marking an important initial step towards understanding these and other rare species from this biome.</p>