Analogues of palytoxin (PLTX), one of the most potent marine biotoxins, are produced by some species of the marine dinoflagellates of the genus Ostreopsis. The proliferation of these species in different coastal zones represents a potential threat of seafood poisoning in humans because the produced toxins can be transferred through marine food webs. Thus, the determination of the concentration of PLTX analogues (ovatoxins-OVTXs, ostreocins-OSTs and isobaric PLTX) in different matrices (seawater, marine fauna, etc.) is necessary to protect human health. This study is addressed to overcome some of the challenges that the chemical complexity of these molecules poses to their quantification by ultra-high-performance liquid chromatography high-resolution mass spectrometry-based techniques (UHPLC-HRMS). In particular, the mass spectra of the palytoxin analogues show the presence of a large number of ions (including mono- and multiply charged ions) whose nature, relative abundances and behavior can lead to quantitation errors if the correct ions are not selected. In this work, the variability of the PLTX and OVTX profiles under different instrument conditions, including the use of diverse electrospray generation sources and different quantitation methods, is studied. Moreover, the extraction protocol in seawater containing Ostreopsis sp. ovata cells is also evaluated. The use of a heated electrospray operating at 350 °C and a quantitative method including ions from different multiply charged species provides a more robust and reliable method for overcoming the problems due to the variability in the toxin's mass spectrum profile. A single MeOH : H2O (80 : 20, v/v) extraction is proposed as the best and reliable procedure. The overall method proposed was applied to quantify OVTXs (-a to -g) and iso-PLTX along the 2019 Ostreopsis cf. ovata bloom. The cells contained a total toxin concentration of up to 20.39 pg per cell.