Chloroplasts originate from an ancient cyanobacterium and still harbor a bacterial-like genome. However, the centrality of Shine-Dalgarno ribosome binding, which predominantly regulates proteobacterial translation initiation, is significantly decreased in chloroplasts. As plastid ribosomal RNA anti-Shine-Dalgarno elements are similar to their bacterial counterparts, these sites alone cannot explain this decline. By computational simulation we show that upstream point mutations modulate the local structure of ribosomal RNA in chloroplasts, creating significantly tighter structures around the anti-Shine-Dalgarno locus, which in-turn reduce the probability of ribosome binding. To validate our model, we expressed a mCherry gene harboring a Shine-Dalgarno motif in the Chlamydomonas reinhardtii chloroplast. Co-expressing it with a 16S ribosomal RNA, modified according to our model, significantly enhances its expression compared to co-expression with an endogenous 16S gene.