The plastid ribosomal protein s16 (rps16) gene was cloned from potato (Solanum tuberosum L. ssp. tuberosum cv Desiree) by PCR amplification to obtain a new homologous recombination site of plastid transformation. The potato rps16 genomic clone was 1627 bp in size and the coding region was interrupted by an 859 bp intron. Exon I was 40 bp, encoding 13 amino acids and exon II was 227 bp, encoding a 76 amino acid polypeptide. The nucleotide sequence of the rps16 gene from the "Désirée" potato shared perfect identity with the sequence from the "Superior" potato in the coding region. Three nucleotide substitutions, two nucleotide insertions, and one nucleotide deletion were found between the intron sequence of both "Désirée" and "Superior" cultivars. The amino acid sequence of the potato rps16 gene showed a high level of identity with rice, maize, tobacco, and mustard (84-94%) and a relatively low level compared with Bacillus stearothermophilus and E. coli (27-28%). Expression of the rps16 gene was strong in chloroplasts and transcripts were detectable in amyloplasts, suggesting that the rps16 gene is active in nonphotosynthetic plastids as well as in photosynthetic plastids. These results indicate that the potato rps16 gene can be used as a new homologous recombination site of plastid transformation for potato cultivars.