The domestication of rice increases the divergence between cultivated rice and its wild progenitor because of artificial selection. However, it remains unknown whether highly diverged loci in rice can be explained by neutral demographic scenarios alone. In this study, we genotyped 45 InDels (insertion/deletion) in two subspecies of Asian cultivated rice (Oryza sativa ssp. japonica and Oryza sativa ssp. indica) and their wild progenitor (O. rufipogon/O. nivara). Among them, 17 loci are highly diverged (F-ST > 0.4) between rice cultivars and their ancestor. We performed coalescent-based simulations on neutral demographic scenarios and found that neutral demography alone could explain the polymorphic profiles on those highly diverged loci between cultivated and wild rice. Therefore, more signatures of selection should be considered when detecting artificial selection in rice.