Plesiomonas shigelloides and Aeromonas spp. are Gram negative bacteria vastly distributed in the environment, being isolated from aquatic ecosystems and terrestrial and marine animals. The South American sea lion (Otaria flavescens) is the most frequent marine mammal of the Chilean coasts, living in beaches, rocks or coastline of rivers. In this work we determined the isolation frequency of P. shigelloides and A. veronii biotype sobria in fecal samples of South American sea lions belonging to a colony established at the urban South coastline of Valdivia River, southern Chile. From the 30 samples under study, P. shigelloides was isolated in 27 (90.0%) and A. veronii biotype sobria in 17 (56.6%). To our knowledge, this is the first report of the isolation of P. shigelloides and Aeromonas spp. from South American sea lions in Chile. However, further studies are needed to clarify if these bacteria play any role in producing disease, or are merely commensals, in these marine mammals.