Objective To study the toxicity and species of the Gymnothorax caused the ciguatera fish poisoning in Xiamen. Methods Epidemiological investigation was conducted and five kind of Gymnothorax were collected from the market and determined by mouse bioassay, Cigua-Check kit and high performance liquid chromatograph y-tandem mass spectrometry (HPLC-MS/MS). The mtDNA were extracted from Gymnothorax, and Ctyb gene segment were amplified using PCR techniques and sequenced. Results The result turned out to be not detected (ND)-0.052 MU/g in muscle, and ND-0.23 MU/g in viscera by mouse bioassay among five species. P-CTX-1 was not detected by HPLC-MS/MS. Five species of Gymnothorax were identified, and the toxic Gymnothorax implicated in food poisoning was Gymnothorax undulates. Conclusion This food poisoning was caused by ciguatoxin-carrying Gymnothorax and the species was determined to be Gymnothorax undulates based on sequence analysis.