Krill is a major source of astaxanthin, which has strong antioxidant activity. Fractions with astaxanthin monoesters and diesters of Antarctic krill Euphausia superba were isolated. Astaxanthin esters were separated by C18-HPLC depending on the number of carbons and double bonds of esterified fatty acid(s). Small amounts of other lipids remained in the samples, but relative molecular masses of carotenoid esters could be measured by field desorption mass spectrometry without fragmentation and interference from contaminant lipids. The fatty acids were determined by calculation of difference between astaxanthin and astaxanthin esters. Only five kinds of fatty acids, dodecanoate, tetradecanoate, hexadecanoate, hexadecenoate and octadecenoate, were detected. Fast atom bombardment mass spectrometry and secondary ion mass spectrometry showed similar spectra. The fatty acid composition in astaxanthin esters was different from those in krill lipids. Therefore, determination of fatty acids in carotenoid esters by a combination of HPLC elution profile and mild mass spectrometry is found to be a useful tool.