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<i>Coccoloba cowellii</i> Britton (Polygonaceae, order Caryophyllales) is an endemic and critically endangered plant species that only grows in the municipality of Camagüey, a province of Cuba. A preliminary investigation of its total methanolic extract led to the discovery of promising antifungal activity. In this study, a bioassay-guided fractionation allowed the isolation of quercetin and four methoxyflavonoids: 3-<i>O</i>-methylquercetin, myricetin 3,3′,4′-trimethyl ether, 6-methoxymyricetin 3,4′-dimethyl ether, and 6-methoxymyricetin 3,3′,4′-trimethyl ether. The leaf extract, fractions, and compounds were tested against various fungi and showed strong in vitro antifungal activity against <i>Cryptococcus neoformans</i> and various <i>Candida</i> spp. with no cytotoxicity (CC₅₀ > 64.0 µg/mL) on MRC-5 SV2 cells, determined by a resazurin assay. A <i>Candida albicans</i> SC5314 antibiofilm assay indicated that the antifungal activity of <i>C. cowellii</i> extracts and constituents is mainly targeted to planktonic cells. The total methanolic extract showed higher and broader activity compared with the fractions and mixture of compounds.