The basic goal of this study is the isolation of some Bacillus isolates from different sources for production of bioactive products such as detection of cellulose(s) and pectinase(s) and identification of these isolates using quantitative real-time PCR (qRT PCR) depending on 16S rRNA gene in each isolate. Nine, six and two isolates were obtained from municipal sewage water, composted rice straw and expired pharmaceutical drugs (Capozide), respectively. Out of nine isolates, only four Bacilli (SW2, SW3, SW6 and SW9) were selected and examined for cellulose(s) and pectinase(s) production, and revealed that only SW2 and SW9 exhibited maximum pectate lyase (PL) and polygalacturonase (PGase) viz. 465.55 and 222.53 (U/mg), respectively. Out of six Bacilli isolates (RS1, RS3 and RS5), only RS3 showed maximum productivity of carboxymethylcellulase (CMCase) viz. 657.21 (U/mg). On the other hand, only one Bacillus isolate out of two was selected ECC2 and exhibited the maximum Avicelase productivity viz. 533.32 (U/mg). TaqMan qRT PCR method was used to detect and quantify the 16S rRNA genes of Bacillus isolates tested. Forward primer Bsub5 F and the reverse primer Bsub3 R were used for the amplification of 16S rRNA of the “Bacillus subtilis group", it is also successful to demonstrate the most similarities of the Bacillus isolates in this study and they are closely related to “Bacillus subtilis group".