The objectives of this study are to collect transgenic fluorescent midas cichlid, and to establish the standard operating procedures of sample processing, extraction, purification and polymerase chain reaction (PCR) technique for the qualitative detection. We designed the specific primers for transgenic fluorescent midas cichlid, and successfully cloned the gene fragments of GFP (green fluorescent protein) by polymerase chain reaction (PCR). The integrity of detection techniques will provide for tracking and management of transgenic aquatic organisms (aquatic genetically modified organisms, aquatic GMOs) in the future to effectively control and mitigate the impact on the environment and enhance the development of the aquaculture industry in Taiwan.