Coccoloba cowellii Britton (Polygonaceae, order Caryophylalles) is an endemic and critically endangered plant species that only grows in the municipality of Camagüey, province of Cuba. Pre-liminary investigation of its total methanolic extract led to the discovery of a promising antifungal activity. The major constituents of the aforementioned extract were glucuronides and glycosides of myricetin and quercetin, proanthocyanidins (tentatively characterized by means of HRMS), as well as epichatechin-3-O-gallate, catechin, epicatechin and gallic acid (tentatively characterized by using HRMS and authentic standards). A UHPLC-ESI-QTOF-MS analysis of the methanol 90% fraction (MeOH90-F) derived from the total extract, allowed the identification of flavonoid glycosides/glucuronides, lignin oligomers, and methoxyflavonoids as the main constituents of that fraction. A combination of flash chromatography, 1D and 2D NMR, and NMR-based machine learning tool “Small Molecule Accurate Recognition Technology” (SMART 2.1, available at https://smart.ucsd.edu/classic) allowed the isolation from MeOH90-F of quercetin and four methoxyflavonoids: 3-O-methylquercetin, myricetin 3,3',4'-trimethyl ether, 6-methoxymyricetin 3,4'-dimethyl ether and 6-methoxymyricetin 3,3',4'-trimethyl ether. This report contributes to a better understanding of the phytochemistry of the genus Coccoloba.