As one of the most productive species, Trichoderma asperellum, especially isolated from marine algae, has contributed a number of new terpenes and nitrogen-bearing compounds, encouraging our continuous efforts to further explore them. Consequently, three new nitrogen-containing secondary metabolites, including cyclo(L-5-MeO-Pro-L-5-MeO-Pro) ( 1), 5′-acetoxy- deoxycyclonerin B ( 2), and 5′-acetoxy-deoxycyclonerin D ( 3) were isolated from the marine alga-derived endophytic fungus Trichoderma asperellum A-YMD-9-2. Their structures and relative configurations were fully elucidated through spectroscopic techniques, mainly including 1D/2D NMR and MS. The absolute configurations of 1 and 2 were ascertained on the basis of X-ray diffraction (Cu K α radiation) and ECD data, respectively. The isolation of these new nitrogen-bearing compounds adds to the structural diversity of marine algicolous Trichoderma spp., and they display potent inhibition against some marine phytoplankton species.