Enormous mountainous forests in Sino-Himalayans and Siberia harbor important avian biodiversity in the Northern Hemisphere. Numerous studies in last two decades have been contributed to systematics and taxonomy of passerines birds in these regions and have revealed various and complex phylogeographic patterns. A passerine species Red-flanked Bluetail Tarsiger cyanurus provided a good system to manifest such evolutionary complexity. The subspecies T. c. cyanurus and T. c. rufilatus (or/and T. c. pallidior), divergent in morphology, acoustics, and migratory strategies are allopatric in Siberia and Sino-Himalayan forests, respectively. The two taxa most likely deserve full species status but rigorous genetic analysis is missing. In this study, multilocus phylogeography based on mitochondrial DNA and Z-linked DNA reveals that T. c. cyanurus and T. c. rufilatus are reciprocally monophyletic with significant statistical support and differ with a large number of diagnostic nucleotide sites resulting substantial genetic divergence. Our finding supports the proposed split of Tarsiger cyanurus s.l. that T. cyanurus and T. rufilatus should be treated as two full species. Whether “pallidior” is a subspecies or geographical form of T. rufilatus is still uncertain. Additionally, these two forest passerine species may have diverged 1.88 (3.25–1.30) Mya, which might be shaped by geographical vicariance due to grassland and desert steppe on the central Loess Plateau during the Pliocene. Taken together, this study and further suggests another independent example of North Palearctic–Sino-Himalayan phylogeographic pattern in Palearctic birds.