In Chad Republic, kernels/grains of Vitellaria paradoxa and Parkia biglobosa are two Edible Non-Timber Forest Products (ENTFP) with high economic value. These products are colonized by un-identified post-harvest fungi that are responsible for high post-harvest losses. The objective of the study was to contribute to the management of the post-harvest diseases of kernels of V. paradoxa and P. Biglosa through natural products. To achieve this, post-harvest fungi were isolated from infected kernels and their pathogenicity tested. Then, antifungal activity of Essential Oil (EO) of Thymus algeriensis and crude extract of African panaxia was carry out by the dispersion method on the agar medium on four pathogenic fungi isolated from the two infected ENTFP. Results showed that V. paradoxa kernels were highly infected (77-95%) compared to P. biglobosa (0.6-2.6%). Fungal species frequently associated with V. paradoxa and P. Biglobosa kernels were: Aspergillus niger (46%), Rhizopus nigricans (17%), Oidium sp (22%) and Cercospora sp (8%); and Oidium sp (55%), A. niger (18%), A. flavus (18%) and Cercospora sp (6%) in V. paradoxa and P. biglobosa respectively. Pathogenicity test was positive with all the species belonging to the genus Aspergillus and with Oidium sp. Essential oil of T. vulgaris at 1.5 �l/ml and the crude extract of African panaxia at 120 �g/ml totally inhibited the growth of the four potential mycotoxigenic fungi tested; their efficacy were significantly comparable (p<0.05) to the reference fungicide (Terazeb). In vivo control of post-harvest diseases with these two natural products is being carry out.