The inter-species variability of contamination by domoic acid (DA), okadaic acid and analogues (OAs) and spirolides (SPX) in mussels, oysters, cockles, carpet shell clams and razor clams was assessed. DA concentrations were measured using both high performance liquid chromatography (HPLC) with Ultra Violet (UV) detection and HPLC coupled with tandem mass spectrometry (HPLC-MS/MS); OAs and SPX were measured using HPLC-MS/MS. Observations showed that for each phycotoxin, the contamination rates are species-dependent and the most contaminated species differ according to the kind of phycotoxin. For DA and SPX, cockles appear to be the most contaminated species whereas mussels seem to be the predominant vector for OAs. The effect of cooking process on DA concentrations was investigated in five different bivalve species by comparing toxin concentrations in whole raw flesh with concentrations in whole cooked flesh. The DA concentration decreased in cooked cockles and razor clams whereas it increased in cooked mussels, carpet shell clams and donax. Thus the impact of cooking is bivalve species-dependent. For OAs and SPX, the cooking process was studied on mussels and resulted in an increase in the toxin concentration because of their lipophilic nature. These results should be taken into consideration in exposure assessments and in the design of regulatory monitoring programs, as the current banning levels based on raw bivalves may over- or under-protect consumers when shellfish are eaten cooked.