The franciscana, Pontoporia blainvillei, is an endemic dolphin off the east coast of South America and is considered the most endangered cetacean in the western South Atlantic. In the present study, we analyzed the muscle tissue of 24 franciscana dolphins found on the coast of Espírito Santo (ES) between 2010 and 2019 to investigate trophic ecology using carbon and nitrogen stable isotope analysis. In addition, 127 prey were analyzed to identify the preferred prey. The most important prey species in the diet of the franciscana dolphins were Trichiurus lepturus, Chirocentrodon bleekerianus, and Pellona harroweri. The franciscana dolphins were grouped into three subareas according to where they were collected throughout the distribution: 1 (North), 2 (Center), and 3 (South). In subarea 1, the preferred prey were Stellifer spp., Isopisthus parvipinnis, and P. harroweri, while in subareas 2 and 3, the prey were similar, changing the order of preference among them (Stellifer spp., T. lepturus, and C. bleekerianus). Finally, we identify two possible ecological groups of franciscana dolphins on the coast of ES, influenced by different carbon sources. Our results improve our understanding of the franciscana dolphin's trophic ecology and habitat use, providing new information and guidelines for species conservation in the region.