Like all ciliates, P. tetraurelia rearranges its genome at each sexual generation during the development of its somatic macronucleus from the germinal micronucleus. The rearrangements include the precise excision of short transposon-derived sequences called IES (Internal Eliminated Sequences). Excision fidelity is essential for half of the paramecium genes that contain at least one IES. The excision of a fraction of them depends on small maternal RNAs bound to Piwi proteins (called scnRNAs) that are produced from the entire germline genome during meiosis. This mechanism poses a problem during conjugation between two strains with insertional polymorphisms: a cell will theoretically be unable to excise an SEI carried by the received paternal allele if this SEI is absent from the maternal allele or if the sequence is too divergent. This thesis shows that polymorphisms do not generate maternal excision defects. However, an unknown mechanism appears to cause excision problems for hemizygous SEIs and may contribute to reproductive isolation.