Marine biofouling is a present and potentially increasing future problem at molluscan culture centres. The problem is highly variable, exists on different scales, and its negative impact on cultured organisms and related economic losses at these centres has not been significantly controlled. One approach to fouling control has been the incorporation of natural substances into anti-fouling paints which inhibit the settlement of common fouling organisms. The main objective of the present study was the isolation of naturally occurring substances from marine bacteria which were inhibitory to the settlement of Ciona intestinalis and Pyura praeputialis, two tunicate species causing serious fouling problems in scallop culture systems in Chile. Numerous bacterial strains were isolated from microfouling on natural and artificial substrates submerged in the sea; of 73 strains isolated, 20% demonstrated inhibitory effects on the settlement of the larvae of the above cited tunicates. The inhibitory substances produced by the active bacteria were extracellular, and could be incorporated in an inert matrix (PhytagelTM) without losing their inhibitory properties. Some properties of the inhibitory substance isolated from bacterial strain Clon Nil-LEM (Alteromonas sp) included thermostability, MW < 3500 Da, peptidase lability (against C. intestinalis), and undiminished inhibitory activity when incorporated in the inert matrix.