The purpose of this study was to test the applicability of the API 20E and API Rapid NFT systems for the identification of some predominant gram-negative and gram-positive bacteria isolated from lab-scale activated sludge treatment systems. In this study, one lab-scale sequencing batch reactor (SBR) and one lab-scale continuous-flow stirred tank reactor (CFSTR) were setup. After both reactors had reached equilibrium, many pure cultures isolated from the activated sludge in both systems were obtained and many morphological, biochemical, physiological tests were conducted to identify each pure culture. The API 20E system is a standardized, miniaturized version of conventional procedures for rapid identification of Enterobacteriaceae and other gram-negative bacteria, and the Rapid NFT kit is used for the identification of the gram-negative, non-fermentative bacteria. Also, a Phillips 300 Transmission Electron Microscope and a Phillips 301 Transmission Electron Microscope were applied to further verify the identification of some genera. According to the results of this study, it has been concluded that some commercial products, such as API 20E system and API Rapid NFT system, can be applied for the identification of microorganisms only at the genus level. Many other additional morphological, biochemical, and physiological tests are always needed to obtain the exact identification of each microorganism at the species level. More advanced technologies such as 16S rRNA may be necessary, however, for a rapid identification of the total bacterial population. In this study, it has also been found that Brevibacterium acetylicum and Pseudomonas vesicularis are two of the most dominant species in the activated sludge of CFSTR system. Gram-positive bacteria such as members of the genus Arthrobacter have shown to be very significant and predominant in the SBR system.