Categorization and identification of biodiversity is key to global food security and integrity. Accurate species identification is relevant to many sectors involved in food production and processing, including for pest identification and management and for food authenticity testing. The usual methods of visual identification of species are often not applicable to food products as morphological characters are often removed during processing. However, methods using DNA analysis enable identifications from immature life stages, or fragmentary remains, and are therefore may be of particular use in the food and agriculture industries. Food fraud is a serious socioeconomic issue that continues to grow due to increasing global trade, and technological innovation for detection as well as perpetrating fraud. Incorrect species labeling of food products is one example of food adulteration that has broad impacts including economic, health, conservation and religious consequences. Molecular techniques, like DNA barcoding, have become part of routine methods for species identification and their implementation in the regulation of market products has begun. Although DNA barcoding provides several advantages over other methods, the ~650 base pair target required for analysis is often too long for recovery from degraded samples, for example in cooked or canned products. In these cases real-time PCR provides an alternative. Design of real-time PCR assays requires particular attention to the haplotype coverage and sequence quality. DNA barcode sequences from the Barcode of Life Data System (BOLD), an online DNA barcode sequence library, are a source of quality sequences available for a wide range of species, particularly those of commercial importance. Therefore, BOLD is a useful resource in the design of successful real-time PCR assays for identification of species in food products as well as other species of interest to the food industry, such as agricultural pests. When endogenous DNA is not available, or provides limited information, synthetic oligonucleotide “barcodes” can be employed for traceability and authenticity testing. This thesis explores the linkages between species identification and product authenticity in the agriculture and food industries and provides a proof of concept for the use and detection of an oligonucleotide tag for traceability of apple juice.