In recent years, there has been an increased interest in Europe and in the USA in grafting watermelon onto bottle gourd, Lagenaria siceraria (Mol.) Standl. In this study, genetic diversity and relationships were examined [using 236 sequence-related amplified polymorphism markers] among 56 United States plant introductions (PIs) of L. siceraria and PIs of important cucurbit crops [including Cucurbita maxima Duchesne (winter squash), Cucurbita pepo L. (squash and pumpkin), Citrullus spp. (watermelon), Cucumis melo L. (melon) and Cucumis sativus L. (cucumber)]. The analysis showed that L. siceraria is distinct and has similar genetic distances to the cucurbit species examined herein. The L. siceraria PIs were assembled into two major clusters. One cluster includes groups of PIs collected mostly in South Asia (India) and a few PIs collected in the Mediterranean region and in Northeast Africa. The second cluster includes groups of PIs collected mainly in Southern Africa and in North, Central and South America, and PIs collected in China, Indonesia and Cyprus. All L. siceraria PIs in this study were susceptible to the southern root-knot nematode (RKN) [Meloidogyne incognita (Kofoid and White) Sandground]. However, several PIs, among them a group of closely related PIs collected in Mexico and Florida, were less infected with southern RKNs. All L. siceraria PIs were infested with whiteflies [Bemisia tabaci (Gennadius)], while several PIs were less infested than others and need further evaluation and selection for developing breeding lines that may be less appealing to this pest. Most of the PIs that showed resistance to zucchini yellow mosaic virus and tolerance to powdery mildew were collected in India and belong to the same phylogenetic groups (PGs). Experiments with L. siceraria PIs representing different PGs showed similar grafting compatibility with watermelon. Findings from this study should be useful for the development of superior L. siceraria rootstock lines with enhanced resistance to diseases and insect pests of cucurbit crops.