Rhinella atacamensis and Rhinella arunco are sister species which, together, are distributed from 25°S to 38°S in Chile. Until recently they were considered to be allopatric, with the dividing line around 32°S, but in 2007 a possible zone of secondary contact was found in the Estero Pupío (32°S). We investigated the species status of adult individuals of three localities along this creek using AFLP markers. Data were analyzed with a Bayesian method that allowed the identification of different types of hybrids in a population. In two of the localities in the lower part of the watershed, the majority of the individuals were identified as backcrosses of hybrids with R. arunco or first generation hybrids, although a few individuals were classified as pure R. arunco. This information, supplemented by mitochondrial sequences and reproductive observations in both the laboratory and in the field, shows that hybridization has been a recurrent phenomenon at these two localities. By contrast, in the third locality, higher in the watershed, we detected a certain amount of nuclear introgression of R. arunco in a population where only individuals with phenotypes and mitochondrial genotypes of R. atacamensis were found. Taken together, the genetic data of the three localities suggest that the hybrid zone is a hybrid swarm which is relatively extensive in the watershed of the creek. Identifying the causes of the apparent spatial segregation of the two species in the Estero Pupío will require additional information.