Grafting is the main means of propagation for watermelon crops. The aim of the present study was to evaluate whether light quality during graft healing variably affects different scion × rootstock genotype combinations. Two watermelon hybrid scions (Sunny Florida F1 and Celine F1) and two interspecific squash rootstocks (Radik and TZ-148) were used, and four scion × rootstock genotype combinations derived. After grafting, we tested seven light-emitting diodes (LEDs), which provided narrow-band red (R) and blue (B); R-B with 36% (36B), 24% (24B), and 12% (12B) blue; 12B with additional far-red (12B+FR); and white (W), in a healing chamber. In three genotype combinations, shoot length, leaf area, and shoot biomass were mainly enhanced under red-blue LEDs, while stem diameter was greater under R. In contrast, dry weight of roots, Dickson’s quality index, and ratio of shoot dry weight/length were variably affected in each genotype combination. From the results, it is concluded that light treatments differentially affected each genotype combination, but some parameters involving biomass production show genotypic dependency.