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Ciguatera Fish Poisoning (CFP) is primarily caused by consumption of tropical and sub-tropical fish contaminated by Ciguatoxins (CTXs). These lipid-soluble, polyether neurotoxins are produced by dinoflagellates in the genera Gambierdiscus and Fukuyoa. While there is no regulatory level in Europe for CTXs, the European Food Safety Authority (EFSA) adopted the United States guidance level of 0.01 μg P-CTX1B eq.kg−1 of fish. This limit is extremely low and requires significant improvement in the detection of CTXs. In this study, we compared analytical protocols based on liquid chromatography coupled to tandem low or high resolution mass spectrometry (LC-LRMS or HRMS) to find the best conditions for sensitivity and/or selectivity. Different approaches such as LC conditions, ion choice and acquisition modes, were evaluated to detect the Pacific-ciguatoxins (P-CTXs) on a triple quadrupole (API4000 Qtrap, Sciex) or a quadrupole time of flight (QTOF 6550, Agilent Technologies) spectrometer. Moreover, matrix effects were calculated using matrix-matched calibration solutions of P-CTX1B and P-CTX3C prepared in purified fish extract. Subsequently, the method performance was assessed on naturally contaminated samples of seafood and phytoplankton. With LRMS, the ammoniated adduct ion used as a precursor ion showed an advantage for selectivity through confirmatory transitions, without affecting signal-to-noise ratios, and hence limits of detection (LODs). As also reported by some studies in the literature, methanol-based mobile phase gave better selectivity and sensitivity for the detection of P-CTXs. While the LOD for P-CTX1B and P-CTX3C met the EFSA recommendation level when using LRMS, the findings suggested careful evaluation of instrumental parameters for determination of CTXs. LODs were significantly higher for HRMS, which currently results in the need for a significantly higher sample intake. Nevertheless, HRMS allowed for the identification of artefacts and may allow for improved confirmation of the identity of P-CTXs analogues. Consequently, LRMS and HRMS are considered complementary to ensure adequate quantitation and identification of P-CTXs.