In tropics, species diversity in agricultural systems is often assessed without distinction between native and exotic species. However, the conservation value of an ecosystem depends on its richness in native species. This study was conducted to determine the conservation value of agricultural systems in Togo megahotspot, one of the species-rich sites in Upper Guinean. Specifically, the study compares fallow systems (FS), coffee systems (COFS), cocoa systems (COCS) to forest relics (FR) on the one hand, and on the other hand the agricultural systems (FS, COFS, COCS) between them base on natives tree species diversity and composition. Sites have been selected to represent different forest lands use types. Plots (n = 233) of different sizes (400, 500 and 625 m²) were used for data collection. In each plot, all living trees (DBH ≥ 10 cm) were counted. Rarefaction, generalized linear models (GLM) and ecological distance approach were used to standardized and compare the data. A total of 183 species were recorded, of which 42% were absent from the agricultural plots. Difference in diversity index were significant between the FR and agricultural systems (p<0.001), but not between agricultural systems (p=0.23). Guineo-Congolian climax and endemic species were seriously under threat. The study poses a real problem of regeneration dynamic of these species in human-dominated landscapes that requires further specific work.