Standardized means of identification of endophytic organisms could become a necessary tool for the discovery and optimization of their vast bioactive metabolites. This study aimed to isolate, identified endophytic fungi from the Root (RT) and Leaves Blades (LB) of Annona senegalensis Pers using molecular techniques and analyzed the crude metabolites using Gas Chromatography-Mass Spectrometry (GC-MS) and Fourier Transform Infrared Spectroscopy (FTIR). Endophytic fungi unknown (RT1), Botryosphaeria laricina (RT2), Didymella macrostoma (RT3) and Oxydothis ragae (LB1) associated with Annona senegalensis Pers were successfully isolated and identified. Based on the 18S rRNA gene sequences, four endophytic fungi, RT1, RT2, RT3 and LB1 were assigned GenBank accession numbers MW672177, MW672178, MW672179 and MW672180 inclusive under submission code SUB7061858. The result showed four endophytic fungi; unknown (RT1), Botryosphaeria laricina (RT2), Didymella macrostoma (RT3) and Oxydothis ragae (LB1). The analysis of the crude metabolites reveals quite several chemical compounds most of which have been documented to have pharmacological activities, including N-hexadecanoic acid (8.34%), linoleic acid ethyl ester (40.5%), 1–H–2–benzopyran–1–one, 6–bromo–5–flouro–3–4–dihydro (4.20%), ethyl oleate (13.8%), methyl stearate (14.45%), 10-octadeconoic acid (16.65%), 3–Allyl–6–methoxy phenol (3.17%), caryophyllene (5.77%), eugenol (3.17%), tridecaenoic acid (18.57%), oleic acid (7.34%) among others. In conclusion, this study has shown that endophytic fungi isolated from Annona senegalensis could be rapidly identified using molecular techniques and their metabolites analyzed using GC-MS and FTIR.