Clostridium perfringens is an anaerobic pathogen of animals and humans and has a highly variable accessory genome, which includes many closely related conjugative plasmids encoding antibiotic resistance or toxin genes that carry the tcp conjugation locus. In addition, these plasmids have putative plasmid partitioning systems related to the parMRC family; in all 10 separate, but related, plasmid partitioning groups, parMRCA-J, have been identified. CN4003 carries plasmid-encoded etx (ε-toxin), cpb2 (β2-toxin), cpe (enterotoxin, CPE) and lam (protease) genes. We have demonstrated conjugative transfer of the etx and cpb2-encoding plasmids; obtaining one transconjugant that encoded the etx gene and four cpb2-positive transconjugants. Sequence analysis of these transconjugants was carried out using the Illumina Miseq. Analysis of one of the cpb2 transconjugants led to the assembly of a contiguous plasmid encoding the cpb2 gene, the tcp locus and a urease operon, as well as a parMRCD allele, as expected from PFGE analysis. However, sequence analysis of the etx positive transconjugant yielded only three sequencing reads that could be mapped to the etx gene. Further analysis indicated that the etx plasmid of CN4003 was highly unstable in our strain 13 recipient background, although sequence analysis of genomic DNA prepared just after the transconjugant was isolated, yielded greater sequence coverage, but was still not sufficient to assemble an intact plasmid. Sequence analysis was also performed on the wild-type strain and a wild-type derivative that had also lost the etx-encoding plasmid, and resulted in the assemblies for the cpe and lam encoding plasmids as well as the identification of a novel parMRC operon encoded by the etx plasmid. In conclusion, the results have shown that not all plasmids are equally stable in different C. perfringens strains and that we have only scratched the surface of the complexity of C. perfringens plasmid biology.