Microfluidic technologies are rapidly being designed and integrated into research, clinical, and forensic laboratories as a cost-effective alternative to benchtop techniques. However, a multitude of security concerns, from assay design to data collection and privacy, remain to be addressed. We modeled several attacks on a simple polymerase chain reaction (PCR) protocol, which is integral to many DNA analysis and identification. After identifying potential vulnerabilities, we performed mock attacks using benchtop techniques to demonstrate the catastrophic impact on the outcome of the DNA-identification process. We also propose a countermeasure solution, in which DNA samples are each uniquely barcoded in advance of PCR analysis, demonstrate the feasibility of our approach using benchtop techniques, and discuss how sample barcoding could be mapped onto microfluidic platforms in the future.