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Cabbage (<i>Brassica oleracea</i>) is an important vegetable crop that is cultivated worldwide. Previously, we reported the identification of two dominant complementary hybrid lethality (HL) genes in cabbage that could result in the death of hybrids. To avoid such losses in the breeding process, we attempted to develop molecular markers to identify HL lines. Among 54 previous mapping markers closely linked to <i>BoHL1</i> or <i>BoHL2</i>, only six markers for <i>BoHL2</i> were available in eight cabbage lines (two <i>BoHL1</i> lines; three <i>BoHL2</i> lines; three lines without <i>BoHL</i>); however, they were neither universal nor user-friendly in more inbred lines. To develop more accurate markers, these cabbage lines were resequenced at an ~20× depth to obtain more nucleotide variations in the mapping regions. Then, an InDel in <i>BoHL1</i> and a single-nucleotide polymorphism (SNP) in <i>BoHL2</i> were identified, and the corresponding InDel marker MBoHL1 and the competitive allele-specific PCR (KASP) marker KBoHL2 were developed and showed 100% accuracy in eight inbred lines. Moreover, we identified 138 cabbage lines using the two markers, among which one inbred line carried <i>BoHL1</i> and 11 inbred lines carried <i>BoHL2</i>. All of the lethal line genotypes obtained with the two markers matched the phenotype. Two markers were highly reliable for the rapid identification of HL genes in cabbage.