Diseases affecting livestock can have a significant impact on animal productivity and on trade of live animals, meat and other animal products, which, consequently, affects the overall process of economic development. The New World screwworm, Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae), is an important parasitic insect pest in Neotropical regions. This species has been successfully eradicated from North and most of Central America by the sterile insect technique, but continues to affect the development of the livestock sector in most Caribbean economies. Here, we provide some insight into the patterns of genetic variation and structure and gene flow of C. hominivorax populations from the Caribbean. Analysis of populations from 10 geographical sites in four islands revealed a moderate genetic variability within the populations. Surprisingly, a high population differentiation was found even in intra-island comparisons between populations. This observation can reflect either highly structured populations resulting from a lack of gene flow or a source–sink dynamic. Our study also suggests that New World screwworm populations can recover very rapidly from population contractions. This is valuable information that should be required prior to any investment in large-scale efforts aiming at controlling this pest.