DNA barcoding is a powerful tool that can be effective for identifying unknown seafood samples when morphological characteristics are unreliable. Additionally, DNA barcoding has proven useful for identifying illegal trade such as commercial seafood fraud, and the technique has advanced such that it can be used to identify even highly processed products such as jerky, dog food, and cosmetics. In Puerto Rico, a popular local fried turnover called “empanadillas de chapín” are allegedly prepared using other fish or meat products as a substitute for the traditional smooth trunkfish (Lactophrys triqueter), known in Spanish as chapín. Sharks and rays are commonly sold for local cuisine; however, it is unknown which species of sharks or rays are being consumed. Driven by these unconfirmed reports of substitutions and the consumption of protected shark species, we sought to identify the prevalence of this allegedly common yet unverified type of seafood fraud, using DNA barcoding. Fifteen fish species were identified as substitutes for chapín including elasmobranchs and imported freshwater species. Furthermore, this molecular forensic technique also identified nine shark species sold as fillets in local cuisine, of which the majority were misidentified to the consumer. The meat source inside these fried turnovers and shark meat products could be identified even after it was cooked and visually unrecognizable. This study demonstrates, for the first time, that rays are being consumed in Puerto Rico, and confirms the report that a variety of native and imported fish are being substituted for chapín in the local cuisine.