The present invention relates to the field of plastid transformation. The invention provides transformation vectors and methods to obtain transplastomic plants or algae having a transformed plastid comprising the steps of introducing into plastids a recombinant nucleic acid molecule or vector, and two phases of selection with first selection phase using a non-lethal compound and a second selection phase using a lethal compound. Alternatively, the dual selection method is conducted simultaneously using a lower concentration of the lethal compound.