The identification of cultivated plant centers of origin is of growing interest since the pioneering work of Nikolaï Vavilov. Cultivated species generally show a high level of genetic diversity in their center of origin, thus identifying these areas would have important implications for the conservation and sustainable management of their genetic resources. We aim to identify the center of origin and to infer recent evolutionary history of one of the most emblematic spice tree species ¬¬– nutmeg (Myristica fragrans; Myristicaceae). The species is thought to originate from the Banda islands (Southern Moluccas archipelago, Indonesia), but this has never been confirmed. We characterized the genetic diversity of this species across the Moluccas archipelago using recently developed nuclear microsatellites markers and whole plastid genome sequences. We found two main intra-specific genetic clusters: one in South Moluccas (Banda and Ambon islands) and another in North Moluccas (Ternate, Tidore and Bacan islands). The latter cluster showed higher genetic diversity than the South Moluccas cluster. We then inferred the demographic history of nutmeg and evaluated different evolutionary scenarios using Approximate Bayesian Computation (ABC) analyses. Populations from South Moluccas show patterns of a recent bottleneck, whereas North Molucca populations did not. Moreover, South Moluccas populations are inferred as ancestral, with subsequent population migration to the North Moluccas during the late Pleistocene to early Holocene period. These results have strong implications for conservation strategies of nutmeg.