Nutmeg (Myristica spp.) is a spice plant of high economic value and the largest contributor to local revenue. The nutmeg commodity is obtained from cultivating and harvesting wild nutmeg, which grows naturally in the forest. Wild nutmeg germplasm has the potential to experience genetic erosion and the loss of important gene sources due to land degradation and deforestation. This research aims to determine the genetic diversity of wild Nutmeg accessions using random amplified polymorphic DNA (RAPD) molecular marker analysis to produce data and information on the characteristics and genetic variability of wild Nutmeg accessions in the forests of Halmahera Island, North Maluku. The results showed that the genetic diversity (DNA) of wild Nutmeg (Myristica spp.) accessions ranged from 13.4% to 83.78%. Accession Wayamli8 and accession Maba-Bicoli21 were detected to have high genetic similarity with Banda Nutmeg (Myristica fragrans Houtt) Ternate Variety 1, namely a nutmeg variety with the best seed and mace quality, so wild nutmeg accession Wayamli8 and accession Maba-Bicoli21 has the potential to become targets for selection and domestication.