Ciguatera fish poisoning (CFP) refers to an illness caused by ingesting fish that have accumulated ciguatoxins (CTXs). CFP frequently occurs in the tropical and subtropical Indo-Pacific Ocean and the Caribbean Sea. In Japan, CFP occurs sporadically but constantly in Okinawa and the Amami Islands. The grouper Variola albimarginata is regarded to be safe for consumption. To assess the real risk of V. albimarginata, we analyzed 133 specimens of the fish in Okinawa using liquid chromatography–tandem mass spectrometry (LC–MS/MS). Ciguatoxin-1B, 54-deoxyciguatoxin-1B, and 52-epi-54-deoxyciguatoxin-1B were detected in 28 specimens (21%). In 11 of these specimens (8%), the CTX levels exceeded the US FDA guidance level (0.01 µg/kg CTX1B equivalent). However, only one fish (<1%) was found to have levels above the recommended level in Japan (0.175 μg/kg CTX1B equivalent). The amount of CTXs in the flesh (280 g) of the most toxic specimen (0.225 μg/kg) did not reach the level needed to cause illness. The CFP risk due to the consumption of this species was thus considered to be low in Okinawa, supporting local belief. The CTX levels in the flesh were positively correlated with standard length, body weight, and age. The total CTX levels significantly fluctuated between the male and the female of the species. The estimated annual catch of V. albimarginata in Okinawa and Yaeyama Islands was 4909 kg or 13,636 fish. As many as 1227 fish had levels over the US FDA guidance level, but only 136 fish had levels above the Japanese recommendation. Risk management based on the Japanese recommendation level seems to be effective in protecting public health and enabling appropriate exploitation of fishery resources.