Baobab (Adansonia digitata L.) is a deciduous non-timber tree species that is facing severe threats from both anthropogenic and climatic pressures across its range states. Additionally, baobab seed oil has been used for many years by local populations as medicine to treat different diseases, beauty, and food purposes. However, consumption of baobab seed oil has been reported to cause health effects emanating from the presence of carcinogenic ingredients known as Cyclopropenoid Fatty Acids (CFPAs). Ecological survey and laboratory analysis were carried out to asses the status of Baobab populations and characterize their fatty acid of seeds clued oil respectively. In ecological survey, stratified random sampling design composed of the three land-use types: strictly protected areas, non-strictly protected areas, and unprotected areas were used to select the grids for the study. Baobabs were sampled in belt transect of 1 km long and a 50 m wide, which were carried out in 337 grids located in three different land-uses types. In the laboratory analysis, the physico-chemical properties were determined according to Official Methods of Analysis of the Association of Official Analytical Chemists. The quantification of fatty acid before and after heating was done by the analysis of derivative fatty acid methyl-esters by using Gas-Liquid Chromatography. Baobab density was found to be highest in strictly protected areas (2.45 ± 1.29) and the lowest in unprotected areas (1.52 ± 1.00). The density of adult, sub-adult and juvenile populations were 1.53 ± 0.105, 0.82 ± 0.149 and 0.33 ± 0.253 plants/ha respectively. Furthermore, the results show bell shaped and inverse J-shaped distributions in the unprotected areas and strictly protected areas, respectively. The number of baobabs damaged was higher than undamaged in all land-use types. There were no significant differences in terms of physico-chemical properties in three different regions. It was found that the baobab crude oil contains mainly twelve essential fatty acids and two different CFPAs. The most abundant fatty acids were Palmitic acid, Oleic acid and Linoleic acid in all the three regions. The major breakdown of CPFAs started at 200 °C that would be the best temperature in the refining process of the baobab oil. The findings from this study are important in understanding the status of baobab populations and CPFAs of their crude oil in different land uses and serve to inform decision akers towards sustainable management of this species. Furthermore, the information from this study is vital in understanding the role of biophysical conditions and land uses in shaping the population persistence of the species in its range areas in Tanzania.