Plastid genetic engineering is a safer, more precise, and more efficient transgene expression system than the nuclear genetic transformation system. It has been widely used in basic research and biotechnology applications as the next-generation transgenic technology in plants. Similar to nuclear genetic transformation, selection markers are needed in plastid genetic engineering to identify ‘true’ transformants and acquire homoplasmy. Because of the high copy number of plastids, maternal inheritance of the plastid genome, and the long process of homogenization of transplastomic plants, the selection markers for plastid genetic engineering are different from those used in the nuclear transformation system. At present, antibiotic resistance genes are the most commonly used selectable markers in the transplastomic selections. However for biosafety reasons, they needed to be replaced with either alternative markers or marker-free systems for the plastid genetic engineering. In this review, we have evaluated and summarized the positive and negative features of the selectable markers and marker elimination strategies commonly used in the plastid engineering research in the literature on plastid genetic engineering research. In addition, we have reviewed the features of the reporter genes used in plastid genetic engineering. We hope this review can help improving the current and developing new selectable markers and marker removal systems, and further promote the development of plastid genetic engineering, especially on the monocotyledonous plants.