Dehalococcoides mccartyi strains RC and KS respire toxic 1,2-dichloropropane to environmentally benign propene. Their genomes were sequenced with Ion Torrent technology, assembled, and annotated. The draft genomes of strains RC and KS were 1.50 and 1.49 Mb in size and carried 1,653 and 1,671 genes, respectively.