Clostridium perfringens causes histotoxic and enteric infections in humans and animals. These diseases are mediated by protein toxins, most of which are encoded on closely related conjugative plasmids of the pCW3 family. Many strains carry multiple toxin or antibiotic resistance plasmids from this family. How can these closely related plasmids be maintained within a single strain of C. perfringens? In many bacteria plasmid partitioning is mediated by a ParMRC system, whereby the ParR protein binds to the parC site on the plasmid. ParM then binds to the resultant ParRparC complex and forms filaments that push plasmids to the opposite ends of the dividing cell. Phylogenetic analysis has shown that there are at least ten different ParMRC partitioning families in C. perfringens. Plasmids with genes from the same ParMRC family have not been observed in a single strain, which suggests that these families represent the basis for plasmid compatibility in C. perfringens. To validate this hypothesis, pairs of plasmids with different combinations of parMRC homologues were introduced into a single strain. The relative stability of each plasmid was monitored over three days in the absence of direct selection. The results demonstrated that plasmids with identical parMRC homologues were not compatible, whereas plasmids that had different parMRC homologues could co-exist in the same cell. Surface plasmon resonance then was used to interrogate key recognition steps between ParR and parC. The results showed that ParR homologues bind efficiently to repeats in their cognate parC sequences, but not to parC sequences from a different family. These data show that the compatibility of related conjugative plasmids of C. perfringens is mediated primarily by their ParMRC-like partitioning systems. The results explain how multiple pCW3-like toxin and antibiotic resistance plasmids are found in C. perfringens isolates that cause toxin-mediated diseases in food production animals.