<jats:title>Abstract</jats:title><jats:p>Radish (<jats:italic>Raphanus sativus</jats:italic> L.) is a typical cross‐pollinated crop that exhibits obvious heterosis. Self‐incompatibility is an important character for F<jats:sub>1</jats:sub> hybrid breeding of radish. Knowledge of the <jats:italic>S</jats:italic> haplotypes of breeding lines is very important for breeders to avoid cross‐incompatibility of the parental lines. In the present study, the <jats:italic>S</jats:italic> haplotypes of 63 radish inbred lines, which were independently cultivated by our research group, were identified by PCR amplification, sequencing and BLAST analyses of the <jats:italic>SRK</jats:italic> and <jats:italic>SLG</jats:italic> genes. Finally, fifty‐four inbred lines were classified into 15 class I <jats:italic>S</jats:italic> haplotypes, including three new types, <jats:italic>RsS‐38</jats:italic>,<jats:italic> RsS‐39</jats:italic> and <jats:italic>RsS‐40</jats:italic>. Additionally, three class II <jats:italic>S</jats:italic> haplotypes were identified in nine radish inbred lines. Partial <jats:italic>SRK</jats:italic> or <jats:italic>SLG</jats:italic> sequences were completed, such as <jats:italic>RsS‐11</jats:italic> Lim (<jats:italic>SRK‐S</jats:italic>), <jats:italic>RsS‐26</jats:italic> (<jats:italic>SRK‐K</jats:italic>), <jats:italic>RsS‐5</jats:italic> Lim (<jats:italic>SRK‐K</jats:italic> and <jats:italic>SRK‐S</jats:italic>) and <jats:italic>RsS‐9</jats:italic> (<jats:italic>SRK‐K</jats:italic>). The identified <jats:italic>S</jats:italic> haplotypes were verified with a cross‐pollination test, and <jats:italic>RsS‐9</jats:italic> has weaker self‐incompatibility than other <jats:italic>S</jats:italic> haplotypes. These information will not only contribute to the production of hybrid seeds but also to the development of new self‐compatible inbred lines, which were advantageous of the production of maintain line and male line in CMS breeding system.</jats:p>