Next- generation sequencing (NGS) technologies have accelerated research efforts in the fields of plant and animal agrigenomics. Especially with multiplex PCR (mPCR), scientists are capable of utilizing NGS to detect and analyze gene sequences in humans, animals, microorganisms, and plants for species authentication, de novo sequencing, and variant identification. Amplicon- based targeted library preparation methods, utilizing mPCR, are preferred by many as the more time and cost-efficient method over hybrid-capture methods. However, there are common drawbacks with amplicon-based methods as well. Multiplex PCR has inherent difficulties such as high background and poor uniformity. We developed a high-performing 2.5hr, one tube, amplicon-based library preparation solution for NGS that addresses and resolves these drawbacks. We present results from experiments demonstrating the robust performance of the Paragon Genomics CleanPlex System that yield libraries with low background, no apparent GC bias, and >95% uniformity with as little as 1 ng of DNA. The system has a limit of detection below 1% and high variant detection accuracy, as well as high mapping and on-target rates over a wide range of target numbers and input DNA amounts.