Antifungal activities of aqueous and ethanolic extracts of propolis produced by three different stingless bee species, namely Heterotrigona itama, Geniotrigona thoracica, and Tetrigona binghami, found in Brunei, against Candida albicans and Saccharomyces cerevisiae strains were evaluated. It was found that aqueous extract of the propolis displayed significant activities against the two fungal strains, whereas the antifungal activity of ethanolic extracts was not observed. T. binghami propolis had the highest antifungal activity, followed by G. thoracica and H. itama propolis. The MIC values also indicated that the aqueous extracts (2500-5000 µgmI.) have stronger antifungal activity than the ethanolic extracts (5000-10000 µg mL), and all the propolis extracts were fungistatic. The brine shrimp nauplii lethality bioassay indicated that the propolis extracts are nontoxic and the cytotoxicity test suggested that the propolis extracts have low anti-amoebic activity against Acanthamoeba sp., much lower than that of chlorhexidine. This study revealed the low antifungal and antiamoebic activities of the aqueous and ethanolic propolis extracts from Brunei stingless bees.