Rhizobacteria was group of bacteria that colonize roots, affect growth and control plant pathogensBased on the results of previous studies, 6 isolates have the best ability to control G. boninense in oil palm seedlings. To determine the ability of these isolates, characterization needs to be done. This study aims to identify the molecular isolates of selected rhizobacteria indigenous that act as biocontrol agents G. boninense. Molecular identification of selected rhizobacteria isolates using the 16S rRNA gene. The results showed that All RBI isolates were identified as different species of Bacillus paramycoides strain MCCC (RZ1A 2.1), Microbacterium paraoxydans strain CF36 (RZ2B 1.1), Bacillus albus strain MCCC 1A02146 (RZ2C 2.1), Bacillus cereus strain JCM 2152 (RZ2E 2.1), Serratia marcescens strain NBRC 102204 (RZ2E 1.2), Bacillus cereus ATCC 14579 (RZ1E 2.1).