Expression vectors for Chlamydomonas reinhardtii chloroplast transformation have been constructed with transcription and translation signals from chloroplast genes. The bacterial aadA sequence, coding for aminoglycoside 3″ adenyl transferase, was inserted in these vectors and introduced into the C. reinhardtii chloroplast by particle gun transformation. The stable tranagenic expression of this foreign protein in the chloroplast confers spectinomycin and streptomycin resistance to the transformed cells. This new marker can be used as a reporter of gene expression, and as a portable selectable cassette for chloroplast reverse genetics. Targetted gene disruption mutants of loci required for photosynthesis, tscA and psaC, were thus obtained. A gene disruption of an unidentified open reading frame, ORF472, remained heteroplasmic, suggesting that it has a vital function.