Mycoflora associated with the pod rot disease of cocoa (Theobroma cacao) and evaluation of the in vitro efficacy of aqueous and ethanolic extracts of A. conyzoïdes and Chromolaena odorata against the pathogenic fungi, C. gloeosporioides and B. theobromae, isolated from cocoa pods were investigated. After isolation, the fungal species were exposed to various concentrations (5 ; 10 ; 15 ; 20 mg/ml) of aqueous, and ethanolic (1.25 ; 2.5 ; 5 ; 10 mg/ml) extracts. Results obtained showed some variations in isolation frequency of fungi from cocoa pods of each locality. Aspergillus, Colletotrichum, Botryodiplodia, Trichoderma and Verticillium were the most common genera that colonized the cocoa pods from Akonolinga and Tonga with different incidences. Colletotrichum gloeosporioides was present (48.84%) in pods collected in Tonga and in those from Akonolinga (41.46%), followed by Botryodiplodia theobromae which was present on 20.93% and 29.27% respectively. All the used concentrations of extracts of both plants significantly reduced the growth of the fungal pathogens. For ethanolic extracts, Ageratum conyzoïdes completely (100%) inhibited the growth of both fungi at 10 mg/ml and for Chromolaena odorata, total (100%) inhibition was observed on B. theobromae at 5 mg/ml while C. gloeosporioides was completely inhibited at 10 mg/ml. In the case of aqueous extracts, Chromolaena odorata, completely (100%) inhibited the growth of B. theobromae and C. gloeosporioides at 20 mg/ml. Similarly, Ageratum conyzoïdes completely suppressed the growth of B. theobromae at 20 mg/ml, however, this dose was obtained as an inhibition of 78% of C. gloeosporioides. Further investigation of the isolation of active antifungal compound should be done.