Valid identification of microorganisms is a vital information to establish culture collections. Currently, molecular approach based on 16S rDNA is widely used for bacterial identification. This approach  is however, time consuming and expensive. Matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) allows the identification of microorganisms directly from colonies and it only takes some few minutes. The interest of this study was to identify endophytic bacteria associated with Curcuma zedoaria based on protein profile using MALDI-TOF MS system and compare with 16S rDNA sequence results. Endophytic bacteria were isolated from part of medicinal plant C. zedoaria collected from Bogor, West Java Indonesia. The identification of selected bacteria was performed by protein profile using MALDI-TOF MS. A total of 66 endophytic bacteria from C. zedoaria plant, were selected for identification. The result of MALDI-TOF MS analysis showed that eleven isolates (16.67%) were correctly identified to the species level and 23 isolates (34.85%) matched on genus level of molecular approach. These results demonstrates that the MALDI-TOF system is suitable and feasible approach for the bacterial identification, mainly for screening and grouping of large number isolates.