This paper reports on a novel DNA sequence located at the mitochondrial control region (D-loop) of the white-nest swiftlet (Aerodramus fuciphagus). This hypervariable control region sequence is potentially useful for studying genetic relationships among the white-nest swiftlet populations. The isolation of the control region involves a primer walking technique, which is simple, fast and cost-effective. In this study, the variability of the control region was assessed and discussed.