This dataset contains NCBI data numbers of microsatellite (SSR) data used to assess the genetic diversity of Ocotea quixos (Ishpingo), a socioeconomically important tropical tree species subject to harvesting pressure. The data were generated to evaluate the impact of exploitation on genetic variability and population structure, with the aim of informing conservation and sustainable management strategies. By comparing genetic diversity across individuals from exploited populations, this dataset provides insights into potential genetic erosion, population differentiation, and the resilience of natural populations under anthropogenic pressure. Methods Overview Genomic DNA was extracted from leaf tissue and individuals were genotyped based on these microsatellite (SSR) markers. Genetic diversity and population structure were assessed using standard population genetic approaches. Related publication This dataset is associated with the study:Draper D, Riofrío L, Naranjo C, Marques I. Genetic Diversity of Ishpingo Exploited Trees (Ocotea quixos (Lam.) Kosterm, Lauraceae). Environmental and Earth Sciences Proceedings. 2024; 31(1):6. https://doi.org/10.3390/eesp2024031006