Capybaras are rodent widely distributed in South America, which inhabit lakeside areas including ecological parks and urban sites. Due to anthropological interaction, monitoring zoonotic pathogens in wildlife is essential for One Health. We investigated faecal samples from capybaras living in an urban area in Rio Branco (Acre, Brazil) for the presence diarrhoeagenic E. coli. Virulence factors from shiga toxin‐producing E. coli (STEC), enterohaemorrhagic E. coli (EHEC), and enteropathogenic E. coli (EPEC) were screened by PCR. We detected at least one virulence factor in 81% of the animals, being classified as STEC and EHEC pathotypes. The presence of zoonotic E. coli in capybaras is a warning due to the highly frequent anthropological interactions with wild animals in this area. Our findings highlight the importance of investigating wild animals as carriers of zoonotic E. coli, requiring further investigations into wildlife surveillance and epidemiological monitoring.