The 20 amino acids, except for methionine and tryptophan, are coded for by two to six codons called synonymous codons. Synonymous codons are used differently by different organisms. Hence, codon selection should be important to express recombinant proteins in tobacco chloroplasts. We present here the codon usage table from the entire 79 mRNAs from tobacco chloroplasts. As codons function on mRNAs, codon usage tables should be constructed from mRNAs but not from genes. We devised an in vitro assay for translation efficiencies of codons, and measured the translation efficiencies of several synonymous codon groups in tobacco chloroplasts. Our results indicated that translation efficiencies of individual codons are not always correlated with codon usage. Based on these data, we discuss on synonymous codon selection for expression of inserted genes in tobacco chloroplasts.