Ciguatera Fish Poisoning (CFP) is primarily caused by ingesting reef fishes contaminated with ciguatoxins (CTX) produced by the Gambierdiscus species. The unpredictability of this type of food poisoning poses risks to public health and adversely affecting the fish trade industry. This study aimed to provide useful information on ciguatera in the Philippines. Different reef fish species and host-macroalgae for benthic dinoflagellates were collected in Visayan and Sibuyan Seas. Ciguatoxins were extracted from reef fish samples, and toxicity was determined qualitatively using mouse bioassay. Meanwhile, cell density estimation of toxic benthic dinoflagellates isolated from the host-macroalgae was done through microscopy. It was observed that 4.46% of the total reef fish samples were positive with ciguatoxins. Spatially, Carles, Iloilo in Visayan sea had the highest number of toxic specimens belonging to Epinephelus merra, Lethrinus lentjan, Lutjanus campechanus, Scarus quoyi, Siganus guttatus, and Sphyraena barracuda. Based on data gathered from three sampling sites, fish toxin occurrence is observed to be site-specific. Geographical conditions affect the frequency of toxic samples. Moreover, fish weight is not a good predictor of fish toxicity. For toxic benthic dinoflagellates, Gambierdiscus spp. were observed to have the lowest cell density count among other dinoflagellates averaging 7-115 cells per 100 g macroalgae. On the other hand, Ostreopsis spp. had the highest average cell density of 118-1,455 cells per 100 g macroalgae, followed by Prorocentrum spp. (207-594 cells per 100 g macroalgae). Fish toxicity is directly proportional to the occurrence of benthic dinoflagellates in areas as seen during dry season. Monitoring and management of CFP on identified reef fish vectors and its causative benthic dinoflagellates in the area are necessary to promote food safety and fair trade practice.