Tree bark is one of the potential niches in the tree canopy that supports a variety of fungi, including water borne hyphomycetes. Surveys have been carried out to assess the conidia of water borne hyphomycetes in stemflow and throughfall of several tree canopies in different geographic zones. This study assessed the assemblage and diversity of conidia of water borne hyphomycetes in stemflow by filtration and latex trap (Ficus latex smear on the microscopic slides) methods for Acacia and Ficus tree species for up to four days during the monsoon season. Air temperature, humidity and physicochemical features of stemflow between the tree species did not differ drastically. Conidia of 52 species were recorded in stemflow of two tree species using both methods with 21 common species, while 8 and 23 species were confined to filtration and latex trap, respectively. The species richness and diversity observed were higher in Ficus than Acacia in the filtration method, while it was the opposite for the latex trap method. Although filtration showed lower species richness than the latex trap method, the conidial count was higher in the filtration method than in the latex trap method. Stemflow filtration as well as the latex trap method showed a higher number of staurosporous conidia than other conidial types. The conidia of the top five species found in the filtration and latex trap methods were Anguillospora longissima, Cylindrocarpon aquaticum, Flagellospora curvula, Triscelophorus acuminatus and T. konajensis. This study demonstrated about 50% uniqueness in species of water borne hyphomycetes between the tree species as well as among the methods.