There are certain animal candidates for which researchers have long speculated as having been managed, or possibly domesticated, by indigenous peoples in the pre-Columbian Caribbean, the primary candidate being some members of a group of caviomorph rodents known as hutia (Capromyinae). This study comprises an isotopic and morphological investigation of the potential management of an extinct species endemic to Hispaniola, the Puerto Rican hutia (Isolobodon portoricensis). For comparisons, isotopic analysis was conducted of bone collagen samples examining carbon (∂13Cco) and nitrogen (∂15N) values of I. portoricensis with two other species of endemic hutia, guinea pig (Cavia porcellus), Antillean slider (Trachemys stejnegeri), rhinoceros iguana (Cyclura cornuta) and edible rat (Brotomys sp.) from four sites in the Dominican Republic: El Flaco, El Carril, El Cabo and La Entrada. This data was compared to human and dog collagen values available from El Flaco to assess similarities between these groups. Osteometric data was recorded for hutia mandibles, allowing for body mass estimations (n = 230). The findings suggest that some Isolobodon portoricensis specimens possessed carbon (δ13Cco) values similar to humans and dogs at El Flaco, possibly associated with the consumption of agriculturally produced maize. This research does not indicate whether domestication or management of this species was occurring, at least not in a systematic way. Concurrence with palaeoenvironmental and zooarchaeological data from the region in which El Flaco and El Carril are located indicate that indigenous agricultural practices may have affected populations of hutia, perhaps by attracting them and supporting them within anthropogenic mosaic landscapes. The data also suggests that some degree of either purposeful feeding or scavenging from human agricultural plots was occurring and supports some degree of commensalism between humans and Puerto Rican hutia at these sites.