Pigments of the meso- and bathypelagic chaetognaths Sagitta macrocephala and Eukrohnia fowleri were studied by chromatographic analysis. Supplementary histological studies were also performed. Fat-soluble properties and absorption spectra of the chaetognath pigments indicated that all pigments were carotenoid, independent of chaetognath species or habitat. The major carotenoid in chaetognaths was very soluble in nonpolar solvents such as carotenes, although its absorption spectrum formed a single broad peak at around 460 nm. The characteristics of the carotenoids in the chaetognaths were different from those of the pigments in the plankton which formed their diet. It is therefore inferred that carotenoids in chaetognaths are not formed by the deposition of food pigments in the intestinal tissue, but are synthesized by the chaetognaths themselves.