The mouse bioassay and high performance liquid chromatography (HPLC) post-column oxidation method are different methods of quantifying paralytic shellfish poisoning toxins. In this study, we compared their ability to accurately quantify the toxicity levels in two types of field sample (oysters and mussels) with different toxin profiles for routine regulatory monitoring. A total of 72 samples were analyzed by both methods, 44 of which gave negative results, with readings under the limit of detection of the mouse bioassay ($40{mu}g/100g$ saxitoxin [STX] eq). In 14 oysters, the major toxin components were gonyautoxin (GTX) 1, -2, -3, -4, -5, decarbamoylgonyautoxin-2 (dcGTX2), and decarbamoylsaxitoxin (dcSTX), while 14 mussels tested positive for dcSTX, GTX2, -3, -4, -5, dcGTX2, neosaxitoxin (NEO), STX, and dcSTX. When the results obtained by both methods were compared in two matrices, a better correlation ($r^2=0.9478$) was obtained for mussels than for oysters ($r^2=0.8244$). Additional studies are therefore needed in oysters to investigate the differences in the results obtained by both methods. Importantly, some samples with toxin levels around the legal limit gave inconsistent results using HPLC-based techniques, which could have a strong economic impact due to enforced harvest area closure. It should therefore be determined if all paralytic shellfish poisoning toxins can be quantified accurately by HPLC, and if the uncertainties of the method lead to doubts regarding regulatory limits.