Common buckwheat (Fagopyrum esculentum) is a heterostylous self-incompatible (SI) species with two different flower morphologies, pin and thrum. The SI trait is controlled by a single gene complex locus, S. Self-compatible (SC) lines were developed by crossing F. esculentum and F. homotropicum; these lines have an SC gene, S^h, which is dominant over the s allele and recessive to the S allele. S-ELF3 has been identified as a candidate gene in the S locus and is present in the S and S^h but not s alleles. A single-nucleotide deletion in the S-ELF3 gene of the S^h allele results in a frame shift. To develop co-dominant markers to distinguish between S^hS^h and S^hs plants, we performed a next-generation sequencing analysis in combination with bulked-segregant analysis. We developed four co-dominant markers linked to the S locus. We investigated the polymorphism frequency between a self-compatible line and leading Japanese buckwheat cultivars. Linkage between a developed sequence-tagged-site marker and flower morphology was confirmed using more than 1000 segregating plants and showed no recombination. The developed markers would be useful for buckwheat breeding and also to produce lines for genetic analysis such as recombinant inbred lines.