Bioactivity-guided fractionation of the separate CH2Cl2 extracts from the aerial parts of Peperomia alata and P. trineura yielded seven polyketides: alatanone A [3-hydroxy-2-(5'-phenylpent-4'E-enoyl)cyclohex-2-en-1-one, 1a] and alatanone B [3-hydroxy-2-(3'-phenyl-6'-methylenedioxypropanoyl)cyclohex-2-en-1-one, 2a] from P. alata and trineurone A [3-hydroxy-2-(11'-phenylundec-10'E-enoyl)cyclohex-2-en-1-one, 1b], trineurone B [3-hydroxy-2-(15'-phenyl-18'-methylenedioxypentadecanoyl)cyclohex-2-en-1-one, 2b], trineurone C [3-hydroxy-2-(17'-phenyl-20'-methylenedioxyheptadecanoyl)cyclohex-2-en-1-one, 2c], trineurone D [3-hydroxy-2-(hexadec-10'Z-enoyl)cyclohex-2-en-1-one, 3a], and trineurone E [(6R)-(+)-3,6-dihydroxy-2-(hexadec-10'Z-enoyl)cyclohex-2-en-1-one, 3b] from P. trineura. The isolated compounds were evaluated for antifungal activity against Cladosporium cladosporioides and C. sphaeospermum and for cytotoxicity against the K562 and Nalm-6 leukemia cell lines.