Abstract: Background and Objective: The utilization of biological control agents using microorganisms is considered as one of the safest and most affordable strategies. This study was conducted to investigate the antagonistic potential of endophytic bacteria against Phytophthora palmivora causing black pod rot disease on cocoa in Indonesia. Materials and Methods: Endophytic bacteria were explored from healthy cocoa pods in Java, Sulawesi and Papua islands. Their antagonistic potential was screened using dual culture method. Bacterial isolates combating the growth of P. palmivora were grouped using rep-PCR technique (BOX1A, ERIC and REP primers). Their inhibition consistency was examined against P. palmivora using double layer technique. Histological assay on mycelial of pathogen was performed under SEM. The DNA of representative isolates was molecularly sequenced according to 16S rRNA and gyrB genes. The effectiveness of their antagonism under in vivo assay was observed on the P. palmivora-inoculated healthy cocoa pods. Results: The growth of P. palmivora was totally inhibited by 127 isolates. The clustering with rep-PCR assay revealed 12 groups of isolates which were independent on cacao clones, orchards and geographical origins. Several isolates showed the inhibition zone under double layer test. SEM viewed morphological abnormality as well as hyphal lysis, shrinking and wrinkling. The representative isolates were identified as members of Achromobacter, Alcaligenes, Bacillus, Burkholderia and Sphingobium genera. The optimum inhibition under in vivo experiment was exhibited by B. subtilis. Conclusion: The explored antagonists have possibility as alternative sustainable disease management strategy under appropriate formulation and application techniques as well as favourable environmental condition.