Bottle gourd is an important cucurbit crop worldwide. To provide more available molecular markers for this crop, a bioinformatic approach was employed to develop insertion–deletions(In Dels) markers in bottle gourd based on restriction site-associated DNA sequencing(RAD-Seq)data. A total of 892 Indels were predicted, with the length varying from 1 bp to 167 bp. Single-nucleotide In Dels were the predominant types of In Dels. To validate these In Dels, PCR primers were designed from 162 loci where In Dels longer than 2 bp were predicated. A total of 112 In Dels were found to be polymorphic among 9 bottle gourd accessions under investigation. The rate of prediction accuracy was thus at a high level of72.7%. DNA fingerprinting for 4 cultivars were performed using 8 selected Indels markers, demonstrating the usefulness of these markers. To provide more available molecular markers for this crop, a bioinformatic approach was employed to develop insertion-deletions (In Dels) markers in bottle gourd based on restriction site-associated DNA sequencing (RAD-Seq) data. A total of 892 Indels were predicted, with the length varying from 1 bp to 167 bp. Single-nucleotide In Dels were the predominant types of In Dels. To validate these In Dels, PCR primers were designed from 162 loci where In Dels A total of 112 In Dels were found to be polymorphic among 9 bottle gourd accessions under investigation. The rate of prediction accuracy was thus at a high level of 72.7%. DNA fingerprinting for 4 cultivars were performed using 8 selected Indels markers, demonstrating the usefulness of these markers.