We previously reported that high level of reporter gene transcript does not confer high amount of reporter protein accumulation in Chlamydomonas reinhardtii chloroplast transformants. Here, to further clarify the correlation between the level of transcript and protein accumulation, we generated the beta-glucuronidase (GUS) reporter gene (uidA) constructs with different potential for translation efficiency of the GUS protein by incorporating different 5' and 3'-untranslated regions of chloroplast genes into each construct. The relationship between mRNA stability and translation efficiency of the GUS reporter gene in each construct were then studied in C. reinhardtii stable chloroplast transformants. We found that sequences of the two nucleotides immediately upstream of the initial codon were important for translation efficiency and that transformants showing high GUS activity accumulated lower level of uidA transcripts than the transformants with low GUS activity. Moreover, accumulation and half-lives of these chimeric-uidA transcripts were increased to the same level in the presence of translation inhibitor. The accumulation and/or half-lives of several endogenous chloroplast transcripts were also increased by such inhibitor. Collectively, our results indicate that efficient translation destabilizes transcripts in chloroplasts of C. reinhardtii, and that there is an apparent negative correlation between protein accumulation and mRNA stability.