With 9 maternal heritable chloroplast gene fragments (atpA, atpB, matK, petA, psaA, psbA, psbB, psbC, and rbcL), we explored the lineage relationships of 3 BBCC genome allotetraploids and 5 related BB or CC genome diploids in the Oryza genus. Further phylogenetic analyses indicated that the 3 allotetraploid species did not originate from a common speciation event but occurred at least 3 times in different distribution areas. The maternal parent of the tetraploid O. punctata was possibly the Africa CC genome diploid O. eichingeri, whereas the maternal parent of O. minuta and O. malampuzhaensis was possibly 2 extinct Asian BB genome diploids. Our results provided important molecular evidence to track complicated reticular evolutionary processes for the polyploids and also broaden our understanding of the puzzling speciation histories of flowering plants.