Apicomplexan parasites contain so-called apicoplasts, which are similar to chloroplasts of red algae. Multiple alignments of the 5'-leader regions of plastid-encoded genes revealed several conserved noncoding regions in parasites as well as in red algae. The regions were assumed to be sites for RNA interactions with regulatory proteins. Conserved sites were found upstream of ycf24, which is required for [Fe-S] cluster development, and several other genes. In particular, a simultaneous regulation was predicted for ycf24, rps4, and rpoB in Toxoplasma gondii. The prediction agreed with the known data that apicoplasts are only required for a short time, but confer pathogenicity on T. gondii. Another site was predicted upstream of rpoB, which encodes the β subunit of RNA polymerase, in red algae Porphyra spp. and parasites Eimeria tenella and Theileria parva.