The rocky shore of Punta Este, Golfo Nuevo (Patagonia, Argentina), was sampled by means of the standardized NaGISA (CoML) protocol, that was aimed to generate biodiversity baseline data in six levels, from high intertidal to 10 m depth. Based on the generated data, we analysed the benthic assemblage structure, species richness, mean abundance and the distribution pattern of invertebrate functional groups, typifying species in each intertidal and subtidal level. The intertidal sampled is exposed to extreme physical conditions higher than any other rocky shore system studied, with air temperature variation of 40°C during the year, maximum winds of 90 km/h and semidiurnal tides of 5 m amplitude; on the other hand subtidal presents less thermal variation (ΔT 10°C throughout the year) and more homogeneous physical conditions. We identified 64 taxa represented by six animal phyla: Mollusca, Arthropoda, Annelida (Polychaeta), Echinodermata, Cnidaria and Nemertea; and three algal phyla: Chlorophyta, Rhodophyta and Heterokontophyta (class: Phaeophyceae). Ordination non-metric multidimensional scaling plots showed three different assemblages in terms of species composition (intertidal, subtidal 1 m level and subtidal 5–10 m levels). The intertidal was represented by suspension feeders, mainly Mollusca. The tiny mussels Brachidontes rodriguezii and Brachidontes purpuratus, and the algae Corallina officinalis dominated the intertidal and promote positive interaction (amelioration), preventing other species from the extreme physical stress. The subtidal was mainly represented by grazers. Our results showed a tendency of suspension feeders to decrease and grazers and predators to increase from high intertidal to subtidal, probably driven by decreasing physical stress. The gastropod Tegula patagonica, the sea urchins Arbacia dufresnii and Pseudechinus magellanicus and the invasive algae Undaria pinnatifida were the most abundant species in 1 m–10 m levels. Based on previous work performed in the region, we hypothesize that the differences registered between intertidal and subtidal levels could be explained in part by an increase in physical stress at the intertidal, with low predation pressure that promotes positive interactions, while in the subtidal the increase in consumers and decrease of physical stress could lead to associational defences. Our results could be useful as baseline data to develop a sustainable network for long-term monitoring of benthic community changes due to anthropogenic activities.