Managing microbial contaminants is critical during the manufacturing of biologics, food and beverage to ensure that products meet the high quality product standard as well as staying compliant within the regulatory guidelines. These microbial contaminants may be introduced during the production through contaminated ingredients or from pre-existing microbial biofilm on production equipment and utensils. It is important to identify the microbial contamination often to the species level during investigation, in order to better understand the sources of contaminants and the necessary measures to prevent such contamination. Traditional microbiology culture, biochemistry and staining methods for microbial identification typically take days to weeks to complete, and have limitations in achieving reliable and conclusive results. It has been shown that molecular sequencing is superior in identifying microbes to the species level, when compared against conventional microbiology staining and culture methods. In this presentation, we describe a simple, fast and accurate microbial identification method by sequencing ribosomal RNA gene using the GenomeLab GeXP Genetic Analysis System. Upon isolation of nucleic acid from each microbial sample, the gene target is amplified using polymerase chain reaction (PCR), followed by sequencing reaction utilizing the Dye Terminator Cycle Sequencing (DTCS) on the GeXP. Results are compared against the NCBI microbial library to identify the contaminants. Sequence homology information may also be used for further phylogenetics analysis.