Ciguatera is one of the most widespread food poisonings caused by the ingestion of fish contaminated by ciguatoxins (CTXs). Snapper and grouper with high palatable and economic value are the primary food source and fish species for exportation in the Republic of Kiribati, but they are highly suspected CTX-contaminated species due to their top predatory characteristics. In this study, 60 fish specimens from 17 species of snappers and groupers collected from the Kiritimati Island and Marakei Island of the Republic of Kiribati were analyzed using mouse neuroblastoma (N2a) assay and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to determine Pacific CTX-1, -2 and -3 (P-CTX-1, -2 and -3). The LC-MS/MS results show that CTXs were detected in 74.5% of specimens from Marakei Island and 61.5% of specimens from Kiritimati Island. The most toxic fish Epinephelus coeruleopunctatus from Marakei Island and Cephalopholis miniata from Kiritimati Island were detected as 53-fold and 28-fold P-CTX-1 equivalents higher than the safety level of 10 pg/g P-CTX-1 equivalents, respectively. CTX levels and composition profiles varied with species and location. The N2a results suggested that fish specimens also contain high levels of other CTX-like toxins or sodium channel activators. The distribution patterns for ciguatoxic fish of the two islands were similar, with fish sampled from the northwest being more toxic than the southwest. This study shows that groupers and snappers are high-risk species for ciguatera in the Republic of Kiribati, and these species can further be used as indicator species in ciguatera endemic areas for risk assessment.