Tropomyosin is known to be the main allergen in crustaceans and the objective of this study was to investigate if this protein could be detected in commercial crustacean oils from Antarctic krill (Euphausia superba) and the zooplankton Calanus finmarchicus. We also examined the possibility of determining the protein content in the oils by direct amino acid analysis. Western blotting showed that a commercial antibody against shrimp tropomyosin cross-reacted with a protein of similar size in Antarctic krill and C. finmarchicus. The protein tentatively identified as tropomyosin, was also detected in krill oil products, but not in oils from C. finmarchicus. The acetone-heptane method used for extracting proteins in the oils is however not optimal. Other extraction methods should therefore be considered when investigating the presence of allergenic proteins in oils. Direct amino acid analysis on oils should be further explored as a method for determining the total amount of proteins present.