The Chlamydomonas reinhardtii chloroplast atpB mRNA contains sequences at its 3' end that can form a complex stem/loop structure. Deletions of part or all of this sequence in transformed C. reinhardtii cells led to decreased atpB mRNA accumulation, whereas transcription rates were unaffected. The reduction of mRNA to 20% to 35% of wild-type levels in transformants without 3' stem/loops was correlated with the accumulation of atpB mRNA that was heterogeneous in size. These results indicated that RNA secondary structures function both in mRNA stabilization and in 3' end formation in C. reinhardtii chloroplasts. Furthermore, deletion of the stem/loop resulted in a decrease in the steady-state level of the ATPase beta-subunit to approximately 60% of wild-type levels, suggesting that translational and/or post-translational mechanisms may influence the steady-state level of the atpB gene product.