Ciliates are the model of choice to study RNA interference, the mechanism playing key role in biology of these protists. The genome scanning processes of two ciliates, tetrahymena and Paramecium (oligohymenophorea), leading to formation of the somatic genome from the chromosomes of the generative nucleus are compared in the review. Matching of several simultaneously present in one cell genomes is mediated by small RNAs and results in precise reproduction of maternal somatic genome in the sexual progeny.