Trans-species polymorphisms (TSPs) are fundamental to preserving ancient genetic diversity, yet the evolutionary forces driving their long-term maintenance remain largely unexplored. Here, we investigate genome-wide TSPs in two Cucumis species, cucumber and melon, using whole-genome sequencing data from over 1200 accessions. A total of 5149 TSPs were identified, which predominantly located in genic and promoter regions. Coalescent analysis indicated that both gene flow and balancing selection have contributed to the persistence of these ancestral alleles. Moreover, among the 99 genes with shared coding-region polymorphisms, two genes that cluster by alleles rather than by species provide evidence of long-term balancing selection. These genes are involved in the immune and stress response processes with pleiotropic effects. Our findings elucidate the complex evolutionary forces driving TSPs in Cucumis, providing mechanistic insights into the maintenance of intraspecific genetic diversity in plants across deep evolutionary timescales.