The shallow-water hydrothermal system of Punta Mita in Banderas Bay is located on the fault called Fisura de las Coronas off Punta Pantoque beach. In this area, three sites with hydrothermal vents were studied at a depth of 9 m. This study aimed to characterize the structure of the benthic infauna communities that coexist in this hydrothermal system; therefore, physicochemical parameters were measured and the organisms found in the sediment samples were identified up to the class taxonomic level. The highest temperatures (89°C) were recorded within the hydrothermal influence area, which was reflected in an inverse relationship with pH, conductivity and salinity. Sediment temperature profiles increased at greater depth. A total of 371 individuals were found and these were grouped into eight classes: Malacostraca, Maxillopoda, Gastropoda, Bivalvia, Scaphopoda, Polychaeta, Leptocardii and Stenolaemata. The Malacostraca class was the most abundant with 240 individuals, while the Scaphopoda was the lowest with 3. The organic matter contents in the sediments were higher in the areas adjacent to the hydrothermal activity. The high temperature of the hydrothermal discharges structures the benthic community since it was the factor that differed most significantly in the study sites, causing lower abundances in the area of hydrothermal influence compared with the more distant areas. Despite the above, it is concluded that the benthic community of the area with hydrothermal activity is part of the community adjacent to this influence, only in lower numbers.