If daughter copies of unit-copy replicons recombine with each other, a replicon dimer results that cannot be partitioned equally to daughter cells at cell division. We present evidence that dimer formation interferes with plasmid equipartition in the case of a miniplasmid derived from the unit-copy plasmid prophage of bacteriophage P1. Asymmetric partition occurs, leading to a relatively high rate of loss of the plasmid from the growing population. In contrast, the wild-type P1 plasmid is maintained very efficiently in host cells. We show that this efficient maintenance is due to the presence of the loxP-cre site-specific recombination system present on the intact P1 plasmid. This system promotes rapid recombination between two loxP sites on dimer molecules, resolving them into monomeric substrates for proper partition. We suggest that bacterial replicons that are maintained with great accuracy in recombination-proficient cells might also encode high-efficiency recombination systems.