Island Southeast Asia (ISEA) witnessed extensive human dispersals during the Holocene, yet details of this event remain controversial. The Sulu Archipelago has a protracted history and is home to a great diversity of people, languages, and lifeways, but remains largely unexplored. Human populations with their interactions and movements within and in adjacent regions carried with them their languages, cultures, and genes, along with various domestic animal species including dogs (Canis familiaris), pigs (Sus scrofa), chickens (Gallus gallus), and the commensal Pacific rats (Rattus exulans). These faunas share a parallel history with the human agents that moved them across the region. Current understanding on the prehistoric translocation of these species posits varying migration origins and timings in contrast to previous narratives. Though ubiquitous in the archaeological record of the Pacific islands, chickens still have not been utilised extensively as a bioproxy for understanding early human movements within some Indo-Pacific regions. We seek to characterize contemporary genetic diversity in native chickens in the Sulu Archipelago and compare these populations with those from adjacent regions, including the rest of the Philippines, Indonesia, and the Pacific. We collected feathers from 300 modern chicken specimens from Zamboanga, Basilan, Sulu, and Tawi-Tawi and sequenced the mitochondrial DNA control region (mtDNA-CR). This study demonstrates that there is a sizeable amount of mtDNA-CR genetic diversity and structure in chickens from the Sulu Archipelago. Our findings reveal the potential of chickens as a bioproxy for understanding prehistoric human movement in the region.