Abstract Hevea brasiliensis (rubber tree) is the main source of natural rubber worldwide. In commercial plantations, high‐yield rubber tree clones are propagated by grafting onto seedling rootstocks. In this study, the transcriptomes of the RRIM 600 clone grafted on different rootstocks in southeastern Brazil were evaluated. Exclusively expressed genes (EEGs) and differentially expressed genes linked to quantitative trait loci and coexpression networks were identified. The combination of an RRIM 600 scion (clone) with a non‐clonal PB 235 rootstock resulted in the highest mean yield (76.03 g/tree dry rubber), followed by non‐clonal IAN 873 rootstock (64.30 g/tree dry rubber). In the non‐clonal IAN 873 rootstock combination, we identified the RPD3b gene, an EEG associated with the jasmonate pathway, which increases latex production. This effect was not detected in the non‐clonal RRIM 600 and nonselected seed (NSS) rootstock combination, which resulted in decreased latex production. Distinct coexpression patterns were observed, with scion condition (RRIM 600): PB 235 showing stronger gene aggregation, indicating more synergistic interactions among the rubber‐related genes Hevea rubber transferase, rubber elongation factor, and small rubber particle protein. In contrast, the NSS rootstocks presented a more dispersed pattern and low latex yield. Our findings highlight the importance of initiating rootstock‐breeding programs to improve the production of rubber trees and provide valuable insights into the complex interactions between scions and rootstocks and their impact on latex yield in rubber trees.