One of the processes most used in biotechnology today for handling industrial liquid wastes is biological wastewater treatment. The efficiency and quality of its operation depends on the composition and activity of the microbial community that is present. The application of traditional and molecular techniques has provided a glimpse into the "black box" and has given information to improve the wastewater treatment process. However, bleach pulp and paper mill effluents require a better understanding of the active bacterial population. For the study of these microorganisms, molecular techniques have been used for more than 15 years. However, there has been a lack of knowledge of the physiological requirements and relations with the environment, which seems to be very difficult to obtain involving profile on the diversity. Nowadays, highthroughput sequencing technology is a promising method that makes it possible to identify the entire profile of microbial communities. In combination with fingerprint methods, this approach allows the identification and analysis of the whole biodiversity of microbial communities. In this review, several identification techniques will be discussed.