Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) a nitramine explosive, which has contaminated various military sites during its use, storage and manufacturing worldwide. As RDX is a recalcitrant, less soluble and toxic to human beings and other organisms, it is essential to remediate the contaminated sites. In the current investigation, authors have explored the potential of two indigenous microbes i.e., Bacillus toyonensis (isolate No. WS4-TSB-3, MTCC No. 12857) and Paenibacillus dendritiformis (isolate No. S10-TSA-3, MTCC No. 12859) isolated from an explosive manufacturing facility in north India, for the degradation of RDX in aqueous medium. Furthermore, RDX degradation has been optimized using response surface methodology (RSM) in a 15 days experiment at concentration of 20, 40, and 60 mg/L. It was found that various factors such as initial concentration of RDX, inoculum volume (2, 4 and 6%) and time (5, 10 and 15 days) had impact on transformation and degradation of contaminant. Samples were analyzed using high performance liquid chromatography (HPLC) and intermediate products were identified using LC-MS/MS. Maximum RDX removal of 81.6 ± 1.3 and 84.7 ± 0.9% for Bacillus toyonensis (isolate No. WS4-TSB-3) and Paenibacillus dendritiformis (isolate No. S10-TSA-3), respectively, was observed on 15th day at 40 mg/L initial concentration. During the degradation Hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX), Hexahydro-1,3-dinitroso-5-nitro-1,3,5-triazine (DNX), 4-Nitro-2,4-diazabutanal, Bis(hydroxymethyl)nitramine and nitrite were identified as intermediate products. The findings of the investigation suggest that both the microbes have the potential to degrade RDX in the aqueous medium and can be used for up-scaling the degradation of RDX on explosive contaminated sites.