This study examined two traits related to economic losses in watermelon, resistance to gummy stem blight (GSB) and rind thickness (RTH). QTLseq was used to identify QTL for resistance to GSB isolate 12178A (Stagonosporopsis citrulli) in a population derived from PI 189225. QTLseq identified 4 QTL contributing resistance to S. citrulli, and the QTL on chromosome 5 (Qgsb5.2) was confirmed as a novel QTL. Three watermelon populations were used to investigate the association of fruit size QTL (QFD2.2 and QFSI3.1) with RTH and the rind thickness to fruit diameter ratio (RRP) and to confirm QRTH5.1. Our results indicated that the association of fruit size QTL with RTH and RRP were dependent on their interaction with QRT5.1 and the genetic background of the population. KASP marker assays developed in this study for Qgsb5.2, QFD2.2 and QRTH5.1 should allow breeders to select QTL for resistance to S. citrulli, and for fruit diameter, and rind thickness.