Nutmeg (Myristica spp.) is a high economic value spice crops which is spread on the whole area of Ternate Island, North Maluku province. Nutmeg is generally cultivated using agroforestry system with many varieties of populations and species which is supposed to influence the characteristics of nutmeg plants and micro climate. Thus, understanding the plant characteristics and microclimate of nutmeg plantation using agroforestry system is very important. Nutmeg plantation using agroforestry system is a mix between nutmeg as the main crop with other crops such as cloves, coconut and others. The focus of this research is to understand the characteristics of nutmeg, especially crop production components which cover the number and weight of seeds, microclimate as well as variations of population and diversity. This research employed observation method in which the sample was purposively set as many as 30 plants, using point-centered quarter sampling method. The results showed that agroforestry system affect the characteristics of nutmeg plants and the microclimate. The optimum plant population of 200 plants ha-1 with diversity of 1.38, had higher number and seed weight target -1 than the population of 100 plants ha -1 with diversity of 0.78 or population of 300 plants ha -1 with diversity of 0.82.