Marine sponges are a major component of benthic communities and act as a reservoir for microbial species. In terms of biomass, they are the richest source of secondary metabolite production, with the potential to influence both benthic and pelagic systems. In most cases it is the sponge-associated microbes that account for many of the secondary metabolites assigned to the host. Here we report the occurrence of cycloaspeptide A, a fungus-derived cyclic peptide, in a culturable bacterium Salinispora arenicola. We have also identified nazumamide A, a sponge-derived linear tetrapeptide currently used as a thrombin inhibitor, in Salinispora pacifica. Their structures were determined using an integrated approach consisting of: (1) HPLC-UV-Vis-QToF-MS analysis with multimode ionization (ESI and APCI) and fast polarity switching; (2) database searching and matching of monoisotopic masses, retention times, mass spectra of the precursor and product ions of the compounds of interest and the authentic reference standards thereof.