Abstract Correct assessment of species limits and phylogenetic relationships is a prerequisite for studies in ecology and evolution. Even in well-studied groups such as birds, species delimitation often remains controversial. Traditional avian taxonomy is usually based on morphology, which might be misleading because of the contingent nature of evolutionary diversification. The sand plover complex (genus Charadrius) may be such an example wherein 2 Lesser Sand Plover C. mongolus subspecies groups have been proposed to comprise 2 species. We use genome-wide data of 765K SNPs to show that the widely accepted taxonomic treatment of this sand plover complex appears to be a paraphyletic grouping, with two Lesser Sand Plover subspecies groups found not to be each other’s closest relatives, and with the mongolus subspecies group being the sister taxon of Greater Sand Plover C. leschenaultii. Based on genomic and acoustic analyses, we propose a three-way split of the Sand Plover complex into the Siberian Sand Plover C. mongolus, Tibetan Sand Plover C. atrifrons, and Greater Sand Plover C. leschenaultii. The similar sizes of the Siberian and Tibetan Sand plovers may be the result of niche conservatism coupled with rapid morphological and ecological differentiation in the Greater Sand Plover. Gene flow between the non-sister Tibetan and Greater Sand plovers might have happened in phases of secondary contact as a consequence of climate-driven range expansions. We call for further studies of the Sand Plover complex, and suggest that speciation with intermittent gene flow is more common in birds than currently acknowledged. Lay Summary The use of an integrative approach combining molecular and phenotypic data has revolutionized modern avian taxonomy. Using mitochondrial and genomic-wide variants, we show that the Lesser Sand Plover (Charadrius mongolus) appears to be paraphyletic taxa, with its two subspecies groups (“mongolus” and “atrifrons”) found not to be each other’s closest relatives, and with the “mongolus” group being the sister taxon of Greater Sand Plover Ch. leschenaultii. The pairwise sequentially Markovian coalescent (PSMC) method indicated contrasting demographic histories between the three taxa in the sand plover complex. We further demonstrated that the two subspecies groups in Lesser Sand Plover differ significantly in vocalizations. These evidences suggest that the migratory Palearctic shorebird Lesser Sand Plover should be split into 2 species: Ch. mongolus Pallas, 1776, and Ch. atrifrons Wagler, 1829. Graphical Abstract Graphical Abstract