A method of transforming plant plastids and regenerating fertile transplastomic plants by somatic embryogenesis is disclosed. The method involves transforming a plant plastid in a plant cell capable of being regenerated through somatic embryogenesis with a plastid expression cassette comprising one or more selectable marker genes that express in both green and non-green tissue and in light and dark conditions wherein the selectable marker gene product provides resistance of the plant cell to a selection agent. The transplastomic plant cell is cultured in the presence of the selection agent under conditions to cause the formation of a somatic embryo. The somatic embryo is grown into a fertile transplastomic plant. Preferably, the expression cassette contains two different selectable marker genes that express different proteins that provide plant cell resistance to the same selection agent.