The agouti was one of the many synanthropic species humans translocated to the Caribbean islands from South America by at least AD 35. Here, we apply a genetic commensal model to the medium-size rodent agouti (Dasyprocta sp.) in order to explore interactions among Indigenous peoples in the Caribbean and South America. 26 cytochrome b gene (Cytb) fragments (97 bp to 274 bp) were successfully amplified from 30 archaeological agouti bones from four sites: Sabazan (n = 5) and Grand Bay (n = 19) on Carriacou, Macabou (n = 1) on Martinique, and BK77 Grand Case (n = 1) on Saint Martin. The high success rate and good quality of the ancient DNA (aDNA) sequences demonstrates the potential of the modified silica-spin column method by Yang et al. (1998) for extracting DNA from ancient specimens from tropical climates. Sequence analysis of the obtained fragments advance species identification of Caribbean agouti and knowledge of population structure, providing a strong basis for tracing Indigenous mobility. This paper emphasizes the potential of the commensal model for the study of island interactions and suggests great promise for the continuation of aDNA research in the Caribbean and other tropical regions.