Two new naturally occurring sulfurated diketopiperazines, dehydroxymethylbis(dethio)bis(methylthio)gliotoxin (1) and (3S,6R)-6-(para-hydroxybenzyl)-1,4-dimethyl-3,6-bis(methylthio)piperazine-2,5-dione (2), along with three known analogues (3–5) were isolated from the culture extract of Trichoderma virens Y13-3, obtained from the surface of the marine red alga Gracilaria vermiculophylla. The structures and relative configurations of 1 and 2 were determined by extensive 1D/2D NMR, MS, and IR spectroscopic data, and their absolute configurations were established by analysis of ECD spectra aided by quantum chemical calculations. Compounds 1–5 were evaluated for the inhibition of some marine-derived organisms.