Ecuador is considered one of the most biodiverse countries in the world but currently has one of the highest deforestation rates in South America. Consequently, many species occur in small and fragmented populations, a process that might be further exacerbated in trees due to intensive debark. As a first step to overcome this gap, we used 8 nuclear microsatellites (nSSR) to study the patterns of genetic diversity, population structure, and level of inbreeding of Ocotea rotundata van der Werff (Lauraceae), an endemic tree from South Ecuador with a very scarce population size occurring in fragmented patches of the Neotropical forest. Despite being included in the IUCN Red List as Vulnerable, genetic data that would help conservation efforts and future re-introductions are absent. Most historical locations of this species were not found in recent field trips and only 5 populations were recorded in the South of Ecuador and with a very low number of mature individuals (LOJ n=25; CER n=30; YAN n=30; CAT n=25; ZAM n=10). We compare these individuals with the ones from 2 populations recently described in the North of Ecuador (MAQ n=20, PAC n=20). we show moderate levels of genetic diversity despite forest deforestation and fragmentation. The Bayesian clustering program STRUCTURE found the highest LnP(D) and ΔK values for K = 2. The first two coordinates of the principal coordinate analysis (PCoA) explained 25.9% of the total variation, and populations were spatially separated into the two main groups found by STRUCTURE. Nevertheless, genetic results also indicate the presence of effective gene flow among populations suggesting the presence of random mating. However, one small population (ZAM) showed particularly high levels of inbreeding and low genetic variability, being potentially more prone to extinction. Management plans should concentrate on maintaining this high level of genetic variability through both in and ex-situ conservation actions.