Free-roaming dogs have been present in the Galápagos Islands since the 1830s, but their population significantly increased in the 1900s, posing a threat to wildlife and spreading diseases. Efforts to manage the dog population began in 1981; however, large populations still exist on Isabela and Santa Cruz Islands, with their genetic backgrounds not thoroughly investigated until now. A comprehensive genomic analysis was conducted on 187 modern Galápagos dogs, six historical samples between 1969 and 2003, and data from over 2,000 purebred and village dogs. Findings reveal that contemporary Galápagos dogs are a recent mix of purebred breeds without evidence of a population bottleneck from past culling efforts. Furthermore, historical dogs showed signs of shared ancestry with shepherd dogs. Overall, the study suggests that 1980s culling did not effectively control dog populations and indicates a need for improved population management strategies on the islands to protect endangered species.