DNA barcoding is still a relatively new field of study that is gaining popularity as it becomes more available. But there is no single protocol that works consistently and efficiently. While there are protocols that have been developed and proven to be successful, they are for specific organisms. In this article, I took the approach of focusing on a zooplankton species, Daphnia magna, to develop a protocol that worked consistently for DNA barcoding freshwater zooplankton. A series of experiments was run to optimize each step of DNA barcoding until a control protocol was developed that could be applied to other species of zooplankton. I expect the final optimized protocol to be robust and capable of being applied to different organisms.