Strong genetic incompatibilities exist between two primary rice subspecies, indica and japonica. However, the wild ancestors of rice, O. nivara Sharma et Shastry and O. rufipogon Griff., are genetically compatible. How this genetic incompatibility became established has not been clearly elucidated. To provide insights into the process, we analyzed a pair of hybrid sterility genes in rice, DOPPELGANGER 1 (DPL1) and DOPPELGANGER 2 (DPL2). Either of the two loci can have one defective allele (DPL1- and DPL2-). Hybrid pollen carrying both DPL1- and DPL2- alleles is sterile. To explore the origination of DPL1- and DPL2-, we sequenced the DPL1 and DPL2 genes of 811 individual plants, including Oryza sativa (132), O. nivara (296) and O. rufipogon (383). We then obtained 20 DPL1 and 34 DPL2 sequences of O. sativa from online databases. Using these sequences, we analyzed the genetic and geographic distribution patterns of DPL genes in modern rice and its wild ancestors. Compared with the ancestral populations, DPL1- and DPL2- showed reduced diversity but increased frequency in modern rice. We speculated that the diversity reduction was due to a historic genetic bottleneck, and the frequency had likely increased because the defective alleles were preferred following this artificial selection. Such results indicated that standing variances in ancestral lines can lead to severe incompatibilities among descendants. Haplotype analysis indicated that the DPL1- haplotype of rice emerged from an O. nivara population in India, whereas the DPL2- haplotype emerged from O. rufipogon in South China. Hence, the evolutionary history of DPLs conforms to the presumed multiple domestication events of modern rice.