A lab-on-a-chip for the rapid identification of microbial species has been developed for a water monitoring system. We employed highly parallel DNA microarrays for the direct profiling of microbial populations in a sample. For the integration and minimization of the DNA microarray protocols for bacterial identification, rRNA was selected as a target nucleotide for probe:target hybridization. In order to hybridize target rRNA onto the probe oligonucleotide, intact rRNA extracted from E. coli rRNA was fragmented via chemical techniques in the lab-on-a-chip platform. The size of fragmented rRNA was less than 400 base pairs, which was confirmed by polyacrylamide gel electrophoresis. The fragmented rRNA was also labeled using fluorescent chemicals. The lab-on-a-chip for fragmentation and labeling includes a PDMS chaotic mixer for efficient mixing, operated by flow pressure. In addition, the fragmented rRNA was hybridized successfully on a DNA microarray with sample recirculation on a microfluidic platform. Our fragmentation and labeling technique will have far-reaching applications, which require rapid but complicated chemical genetic material processing on a lab-on-a-chip platform.