Background&#xa0; <p>Nutmeg (<i>Myristica fragrans</i> Houtt.) is a commonly grown spice crop in Sri Lanka. The current study is the first systematic report on morphological and molecular characterization, and species distribution modeling of Sri Lankan nutmeg.</p> Results <p>The study examined 97 nutmeg trees from the main cultivating districts of Kandy, Matale and Kegalle in Sri Lanka, assessing 15 quantitative and 13 qualitative traits. A considerable variation was observed in both qualitative and quantitative traits, involving tree, leaf and fruit morphological characters. Correlation analysis revealed significant (<i>p</i> &lt; 0.05) positive relationships considering quantitative (77.14%) and qualitative trait pairs (11.1%). However, none of the fruit traits (i.e. fruit dimensions, shape and pericarp) were found to be suitable predictors of economically important yield parameters i.e. dry weights of mace, nut and kernel. Though morphological and genetic variations were observed, cumulatively those led to a shallow divergence. This urges the need to expand the gene pool through introduction of new germplasms. Eight nutmeg trees were identified for their superiority based on economically important yield traits i.e. dry weights of mace, nut and kernel. Following further evaluations, these elite trees can be recommended for <i>ex-situ</i> conservation and as mother plants for nutmeg breeding programs. In addition to the main nutmeg cultivation districts, Kandy, Matale, and Kegalle, species distribution modeling identified some areas of Kurunegala and Nuwara Eliya administrative districts of Sri Lanka, as potential areas for cultivation of nutmeg.</p> Conclusion <p>The findings provide critical insights into the genetic diversity of nutmeg in Sri Lanka, aiding in germplasm conservation and crop improvement.</p>