The present study evaluates the effects of different cooking methods (grilling, frying and boiling) on selenium contents of six marine species commonly consumed in Portugal. Forty-two composite samples of sardine, horse mackerel, gilthead seabream, silver scabbardfish, hake and octopus were digested in a microwave system and analysed by electrothermal atomic absorption spectrometry. The described method is adequate for the analysis of selenium in marine species and meets the requirements of validation and quality control. Mean selenium contents in raw species ranged from 0.35 mg kg −1 to 1.24 mg kg −1 . Cooked samples presented mean selenium contents from 0.38 mg kg −1 to 1.85 mg kg −1 in grilled fish, from 1.22 mg kg −1 to 1.28 mg kg −1 in fried fish and from 0.84 mg kg −1 to 0.87 mg kg −1 in boiled fish. No statistically significant differences were determined for selenium levels in raw and cooked samples and in different marine species. Estimated selenium intake agrees well with recommendations and is far below the Upper Tolerable Nutrient Level. This is the first study concerning the evaluation of the effects of cooking methods on selenium contents of marine species consumed in Portugal.