Gypsophila paniculata is the only species in the genus Gypsophila that has been used as cut flowers, and the sequencing of its genome has just been completed, opening a new chapter in its molecular genetic breeding. The molecular marker system is the basis for genetic molecular research in the era of genomics, whereas it is still a gap for G. paniculata. In this study, we constructed a genome-wide InDel marker system of G. paniculata after genome resequencing of another wild-type accession with white flowers. Consequently, 407 InDel markers at a distance of ~2 Mb were designed for all 17 chromosomes. Later, the validation of these markers by PCR revealed that 289 markers could distinguish alleles of the two wild-type alleles clearly. The predicted polymorphisms of two wild-type alleles were then transferred to the commercial cultivars, which displayed a rich polymorphism among four commercial cultivars. Our research established the first genome-level genetic map in G. paniculata, providing a comprehensive set of marker systems for its molecular research.