[Objective] The distributions and relationships between crenarchaeol and chlorin were investigated in the continental shelf of East China Sea. [Methods] Organic chemical methods were used to extract crenarchaeol and chlorin from sediment samples. We used High Performance Liquid Chromatography/Mass Spectrometry to quantify crenarchaeol and High Performance Liquid Chromatography to quantify chlorin.[Results] We found that both crenarchaeol and chlorin were widespread in the continental shelf of East China Sea. Terrestrial inputs had little influence on either crenarchaeol or chlorin. Their absolute contents were correlated significantly (P<0.01) with each other. [Conclusion] The crenarchaeol and chlorin on the continental shelf of East China Sea both had marine origins rather than from terrestrial input. The abundances of crenachaeol and chlorin were correlated significantly, which suggested that crenarchaeol may be used as a potential index for the changes in the surface production of East China Sea during historical times.