The invention relates to a watermelon flesh hardness-related molecular marker Hf2-Indel and application thereof. A marker is designed on the basis of a whole-genome sequence of 97103 and re-sequencing information of PI296341-FR according to an insertion/deletion locus, and the closely linked molecular marker Hf2-Indel is developed by accurately mapping hard flesh genes by virtue of a recombinant inbred line progeny mapping population obtained after hybridization of wild hard-flesh watermelons PI296341-FR and cultivated watermelons 97103. Experiments show that the molecular marker Hf2-Indel can be used for preliminarily screening watermelon flesh hardness varieties to fulfill the aim of molecular assisted selection.