Ocotea quixos, known as Ishpingo, is a tree endemic to the Amazonian rainforests of Colombia, Ecuador, and Peru. The dried flower buds and bark are often used as a spice, known for their cinnamon-like flavor. They are used in various traditional dishes and beverages in the Amazon region. The tree is also a source of essential oils that are used in aromatherapy and natural health products. In Ecuador, the Ishpingo tree faces significant threats due to overexploitation for its valuable spices and essential oils. Additionally, extensive deforestation and land use changes have dramatically reduced its natural habitat. Efforts are being made to conserve wild populations through sustainable harvesting practices and reforestation projects. Understanding and preserving the genetic diversity of Ishpingo is vital for ensuring the species' survival and continued contribution to the ecological and cultural richness of the Amazonian rainforest. Nevertheless, we currently lack comprehensive genetic diversity data. Within this scenario, we developed nuclear microsatellites to analyze the genetic diversity in the known Ecuadorian populations of Ishpingo. The results show low levels of genetic diversity, especially when compared with other Ocotea trees. Inbreeding was common in almost all populations, which can result in reduced reproductive success and fitness in natural populations. Despite these results, some populations still harbor moderate levels of genetic diversity, which is key for the preservation of this species. Implementing breeding programs to enhance genetic diversity, as well as preserving material in seed banks, will be essential in restoration actions.