The methyl esterification of lipids employing supercritical methanol is an environmentally benign method since it does not produce alkaline wastewater, as is the case with conventional methods employing sodium hydroxide. Previous studies have shown that solid base catalysts are effective in decreasing reaction temperatures in the supercritical methanol methyl esterification. We focused on the coccolithophore Pleurochrysis carterae, which exhibits coccolith, i.e., CaCO3 cell walls, and confirmed that the coccoliths acted as a catalyst in the methyl esterification of lipids in P. carterae employing supercritical methanol. To confirm the catalytic effect of the coccolith, the results of the supercritical methanol reaction of extracted lipids from P. carterae without coccolith were compared. The results showed that significant differences occurred, confirming that coccolith of P. carterae acts as a catalyst. To confirm the catalytic effect of CaCO3, the main component of coccolith, the green alga Chlorella vulgaris with cellulose cell walls was used to compare non-catalyst, addition of CaCO3and addition of CaSO4–0.5H2O, which is reported to be effective. The results revealed that the amount of the product obtained from the methyl esterification of fatty acids in C. vulgaris employing CaCO3 was more significant than those obtained without any catalyst or with CaSO4–0.5H2O, indicating the effectiveness of CaCO3 as a catalyst for methyl esterification by supercritical methanol. Coccolithophores, which exhibit CaCO3 cell walls, are desirable raw materials for biofuels because they can function as catalysts.