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Abstract Background Animal social systems can be described through four main components: social structure, social organization, mating system, and care system. Social structure describes the relationships between individuals in a population, while social organization describes the group composition, size, and spatiotemporal variation of a population. We use the frameworks of social structure and social organization to study the social system of Microlophus atacamensis , a lizard found in the rocky intertidal zone along the Chilean coast. The area M. atacamensis inhabits poses specific challenges stemming from their use of two distinct habitat types in the intertidal zone: they forage in the cool areas near the water’s edge and use large rocks in more inland areas for basking and refuge. Methods Our assessment of their social system focused on two separate populations: one to characterize social structure by means of focal observations and social network analysis, and a second to assess social organization via home range and core area analyses. Further, we examined the social system in two habitat types that comprise the intertidal zone: cobble fields and interspersed large rocks. Results Social network analysis revealed an interconnected network with a few highly central individuals. Body size influenced the outcomes of aggressive interactions, with interactions being more common in cobble fields where males had more associates and more repeated interactions than females. Spatial analyses revealed that the social organization of M. atacamensis is characterized by (1) high home range overlap, specifically in the cobble fields and (2) relatively exclusive core areas dispersed across both habitat types. Conclusion A social system is composed of both cooperative and competitive behaviors. While our study focused on competitive interactions, the extent and influence of cooperative behaviors is still unclear and merits future research. We suggest that M. atacamensis has a variable social system in which territoriality on large rocks affects access to stationary resources in that habitat (e.g., basking sites and refuges), while competition in the cobble fields could lay the foundation for a system of dominance relationships controlling access to variable food resources in cobble field areas of the intertidal zone.