ABSTRACT European colonization of the Americas had profound impacts on the indigenous peoples of the Caribbean Basin. The indigenous communities of Saint Vincent and the Grenadines and Trinidad and Tobago, two island nations of the Caribbean Lesser Antilles, endured a European colonial presence for just shy of 500 years. Today, analysis of mitochondrial DNA can help paint a better portrait of pre-Columbian indigenous peoples, including their settlement of the Caribbean Basin and their resistance to European colonialism. To further explore these issues, we conducted analysis of genetic variation in two indigenous communities, the Garifuna of Saint Vincent and the First Peoples’ Community (FPC) of Trinidad. Benn Torres et al. (2015) published their analyses of 65 participants’ samples from both St. Vincent and Trinidad, which were collected during the first of two research expeditions to the islands. For this paper, we analyzed an additional 83 participant samples that were collected during a subsequent research expedition to the region. The results of this study confirmed several trends observed by Benn Torres et al. (2015), namely, that the predominate haplogroups represented by Trinidadian and Vincentian samples are A2 and C1, and that these and other observed haplogroups corroborate historical events or periods. Haplogroups previously unseen in these populations, including indigenous haplogroups B2 and D1 and certain South Asian haplogroups, were also observed, thus adding genetic evidence of a complex history of migration to and admixture within the region. This work thus complements and extends earlier research on genetic diversity in the Lesser Antilles, as well as illuminates the resistance and survival of indigenous Caribbean peoples before, during, and after European colonization and the African Diaspora.