The Patagonian scallop (Zygochlamys patagonica) fishery started in the Argentine Sea after exploratory cruises developed during 1995. Knowledge concerning the habitat requirements involved in the settlement processes of the target species was lacking. The main objectives of this study are to find Z. patagonica spat and to assess the characteristics and distribution of its primary settlement substrate (PSS). We observed under binocular microscope different invertebrate species (potential PSS) collected during 2006 from 125 sampling sites between 37° to 44°S and 83–133 m depth. Spat were found on the hydroid Symplectoscyphus subdichotomus (n = 215) and on adult Patagonian scallops (n = 51, attached to the encrusting sponge Iophon proximum, amphipod, and polychaete tubes in nearly half of the cases). To analyze possible interactions between the benthic assemblage and scallop spat throughout the study area, we performed a faunal analysis including the species considered potential PSS (hydroids and scallops) and potential predators. The analysis showed a unique cluster of species closely associated, with variable abundance of hydroids (higher in samples with spat), scallops, and predators. A particular study in MDQ Area (38°S) shows that the sites where spat was collected presented lower density of potential predators and had been scarcely fished in comparison with the other sites within the area. The availability of PSS should be monitored and areas with dense patches of dichotomous hydroids should be protected from trawling.