Herein, we clarify the structure and relative configurations of two prorocentrolide analogues (1 and 2) isolated from the benthic marine dinoflagellate Prorocentrum lima. The results of NMR spectroscopy show that 1 is prorocentrolide substituted by a hydroxy group at C-4, while the newly isolated compound 2 can be thought of as 1 lacking one ether ring and having one extra double bond. The relative configurations of all stereogenic centers and the configurations of the double bonds in 1 and 2 were determined utilizing ROESY correlations and J-based configuration analysis. Furthermore, 2 was shown to exhibit cytotoxicity against HCT-116 and Neuro-2a cells (IC50 2.2 and 5.2 μM, respectively.