Chemical investigation of a deep sea sediment derived fungus Eutypella sp. MCCC 3A00281 resulted in the isolation of six new thiodiketopiperazine alkaloids, namely eutypellazines N-S (1- 6). Their structures were elucidated on the basis of the extensive NMR and mass spectroscopic analysis, including the ECD data for the determination of absolute configuration. The structures of eutypellazines N-P (1-3) were characteristic of unique spirocyclic skeletons, while eutypellazines N-O bearing a spirocyclic tetrahydrobenzothiophene motif were found from wide type fungus for the first time. The biogenetic generation of the spirocyclic skeletons was postulated. Compounds 3-5 exhibited inhibitory effects against vancomycin-resistant enterococci (VRE), suggesting that they may be the potential inhibitors toward drug resistant pathogenic bacteria after the structural modification.