The high demand for syngnathid species in the traditional Chinese medicine (TCM) trade is drastically affecting seahorse populations worldwide. Powdered seahorse not only represents the main material for the preparation of remedies in either TCM or folk medicine but is also being used to facilitate smuggling and avoid customs authorities in different countries. Here, we present the first primer set and standardized real time quantitative PCR (qPCR) protocol designed for a fast, accurate, sensitive, and reliable identification of one of the most threatened fish species in the world, the Pacific seahorse Hippocampus ingens, using DNA traces from powdered material. Our protocol efficiently detected quantities as low as 0.85 pg of seahorse DNA, showing a high specificity even in the presence of DNA from other non-target fish species. The qPCR protocol reported herein may be utilized as a powerful tool to monitor the illegal domestic trade and international trafficking of H. ingens, not only in poaching hotspot countries such as Ecuador and Peru but also in transit and final market destinations such as Hong Kong and China. In addition, we show photographic evidence of seahorse extraction and trade in northern Peru and southern Ecuador, highlighting the need for increased efforts to protect the Pacific seahorse.