Long-term land cover changes play a significant driver of ecosystem and function of natural biodiversity. Hence, their analysis can be used for evaluating and supporting government plans, especially conservation and management of natural habitats such as sago palm. In Papua Province of Indonesia, sago palm has been stated as one of the priority plants in the Medium-Term Development Plan (R.P.J.M.). However, limited studies have examined this palm in one of the Regencies of Papua Province, namely, Merauke Regency. In this study, we performed remotely sensed data imagery and supervised classification to produce land cover maps from 1990 to 2019. During the study period, twenty-one land cover classes were identified. The six classes of the natural forest consist of primary dryland forest, secondary dryland forest, primary mangrove forest, secondary mangrove forest, primary swamp forest, and secondary swamp forest; thus, fifteen classes of non-forested area. Concerning the sago palm habitat, our study evaluated two different categories (1) based on the land cover scheme from the Ministry of Environment and Forestry and (2) according to the peatland land cover ecosystem in Papua. Based on paired samples t-test, the result indicated statistically significant changes specifically at primary dryland (p-value = 0.015), grassland (p-value = 0.002) and swamp (p-value = 0.007). Twelve from 20 districts of Merauke Regency tend to lose the forecasted natural habitat of the sago palm. Therefore, this study suggests the further need to recognize and estimate the yield of sago palm area in these various ecosystems.