<p><i>Momordica cochinchinensis</i> (Lour.) Spreng., commonly known as gac or sweet gourd, is an underutilized crop with significant nutritional and medicinal value. However, the lack of species-specific molecular markers has hindered its genetic improvement. Insertion–deletion (InDel) polymorphisms represent a valuable class of co-dominant markers, especially when derived from transcriptome data, as they can capture functionally relevant genetic variation. This study reconstructed a high-quality reference transcriptome of <i>M. cochinchinensis</i> using publicly available multi-tissue RNA-seq datasets and systematically identified transcriptome-based functional InDel markers. The assembled transcriptome comprised 66,320 unigenes, of which 9946 harbored 16,053 InDel loci exhibiting length variations from 1 to 35 base pairs. Functional annotation revealed that InDel-containing unigenes were enriched in diverse biological processes and metabolic pathways associated with plant growth and development. In contrast to previously reported markers, which were primarily transferred from <i>M. charantia</i> and related cucurbit species, these InDel markers were developed directly from the gac transcriptome, thereby increasing their species specificity and potential functional relevance. Primer pairs were designed for 1512 medium- and large-sized InDel loci. Experimental validation of a subset of these markers demonstrated high amplification success and substantial polymorphism among cultivated gac accessions collected across Vietnam. The validated markers effectively revealed genetic variation and grouped accessions according to genetic and geographical origin. These transcriptome-derived functional InDel markers represent a valuable genetic resource for genetic diversity analysis, germplasm management, and future molecular breeding initiatives in gac.</p>