In this study, methanol extracts from 25 indigenous Korean corals were prepared and their carotenoid constituents were analyzed by high-performance liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry (HPLC-APCI-MS). Among them, extracts from nine species showed detectable peaks in the HPLC chromatogram at 450 nm and the ultraviolet/visible spectra exhibiting carotenoid-specific characteristics were chosen. The mass data of carotenoid peaks revealed that only peridinin could be identified based on literature comparison and suggested the potential presence of novel carotenoid structures. This is the first reported investigation of indigenous Korean coral carotenoids and further work is needed to explore the carotenoids and their potential roles in the ecosystem of indigenous Korean corals.