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The two most disastrous diseases of Theobroma cacao in Ecuador are caused by the pathogenic fungi Moniliophthora roreri (MR, Frosty pod) and M. perniciosa (MP, Witches' broom). Both diseases are prevalent in Ecuador since its detection in 1916 and 1921, respectively. One hundred and twenty-six isolates were isolated from healthy T. cacao leaves, originated from five nurseries in the Ecuadorian Coast. Isolates were screened in vitro for their stimulation/inhibition of growth of MR & MP. The endophytic fungi influenced the growth of Moniliophthora spp. in different manners, 91/126 of the tested isolates stimulated somehow the colony growth of both pathogens, and only 30 and 5 isolates always inhibited the mycelial growth of MR & MP, respectively. The highest percentage of growth inhibitions against MR was 71%, but quite lower for MP (18%). Only two isolates caused symptoms of chlorosis and necrosis in leaves and fruits Phomopsis spp. (Ascomycota ) and Psathyrella sp. (Basidiomycota ). Twenty-four isolates from 11 taxa caused necrosis only fruits ( Ascomycota : Phomopsis spp. , Phoma sp. , Colletotrichum gloeosporioides s.l. , Fusarium decemcellulare , F. equiseti , F. solani , Nectria pseudotrichia , Pestalotiopsis microspora , Didymosphaeria futilis , Xylaria venosula and Basidiomycota: Ceriporia lacerata ) and four isolates/taxa infected only leaves ( Phomopsis spp. , Pestalotiopsis microspora , Nigrospora sphaerica and one unidentifiable isolate of Xylariaceae sp. ). The non-pathogenic isolate, Hypoxylon investiens , inhibited MR in 71%, but also stimulate the growth of MP in 3%. The second-best isolate ( Lasiodiplodia theobromae ) only inhibit MR and MP in 58 y 15%, respectively; and, although the isolate was not pathogenic, the specie is risky to develop a biological control agent. There was no promising isolate against both MR & MP.