Propolis is one of bee’s product which harboring many biological compounds including flavonoid. Considering all biological aspects in oral medicament development, both benefit and biocompatibility issues must be confirmed. Enterococcus faecalis and Porphyromonas gingivalis are known to be the critical oral pathogenic bacteria which are responsible for endodontic failure and periodontal diseases respectively. The purpose of this study was to investigate the effect of ethanolic propolis compound from Apis Trigona towards bacterial growth and cytotoxicity. Propolis Apis Trigona was taken from local apiary in Nglipar sub-district of Yogyakarta, Indonesia and was extracted using maceration procedure. Enterococcus faecalis and Porphyromonas gingivalis were used for bacterial growth evaluation, while fibroblast cells were used for cytotoxic analysis. One way Anova, Kruskal Wallis and Pearson tests were performed for statistical analysis. All treatments were performed in triplicate experimental design. The variances analysis showed p=0.000 and p=0.009 for the effect of ethanolic propolis which indicated potential results, while Pearson correlation coefficient showed the score -0.673 which indicated strong negative correlation. Taken together, these results suggested that the higher bacterial inhibitory capacity, the lower cells viability on the contrary. Further investigations are required for gaining the optimum benefit from propolis Apis Trigona in a higher biocompatibility