Cochliomyia Townsend includes several abundant and one of the most broadly distributed, blow flies in the Americas, and is of significant economic and forensic importance. For decades, Cochliomyia hominivorax (Coquerel) and C. macellaria (Fabricius) have received attention as livestock parasites and primary indicator species in forensic entomology. However, C. minima Shannon and C. aldrichi Del Ponte have only been subject to basic taxonomy and faunistic studies. Here we present the first complete phylogeny of Cochliomyia including numerous specimens per species, collected from 13 localities in the Caribbean. Four genes, the mitochondrial COI and the nuclear EF-1α, 28S rRNA, and ITS2, were analyzed. While we found some differences among gene trees, a concatenated gene matrix recovered a robustly supported monophyletic Cochliomyia with Compsomyiops Townsend as its sister group and recovered the monophyly of C. hominivorax, C. macellaria and C. minima. Our results support a close relationship between C. minima and C. aldrichi. However, we found C. aldrichi containing C. minima, indicating recent speciation, or issues with the taxonomy of the group. We provide basic information on habitat preference, distribution and feeding habits of C. minima and C. aldrichi that will be useful for future forensic studies in the Caribbean.