The dinoflagellate Lingulodinium polyedrum shows circadian expression of proteins. Analysis of the expression profile of ca. 900 proteins (pI range 5-8; MW 22,000-120,000) by chronological proteomics in 12:12h light-dark ('day-night') cycles revealed 28 with quantitative circadian changes. The patterns were classified into three types: Phase 1 ('evening'), Phase 2 ('night'), and Phase 3 ('midnight'). Peptide mass fingerprinting identified luciferin-binding protein in Phase 2 and two components of the tricarboxylic acid cycle in Phases 1 and 2. Thus, rhythmicity appears to be related to physiological states and to control the metabolic pathway in L. polyedrum.