Clostridium perfringens causes severe disease in a wide array of animal hosts but is also carried asymptomatically in many contexts. Extensive experimental analysis has identified key toxinotypes, with multiple genomic studies highlighting substantial genetic similarity between isolates. Despite these insights, existing analyses include only limited isolates from key toxinotypes and frequently exclude accessory genes, such as genes encoded by the many toxin-encoding plasmids found within this species. This study expanded the collection of high-quality C. perfringens genomes to 453 by adding 104 new genomes, including genomes from rarely sequenced toxinotype B, C, D, and E isolates. Both core and accessory genes were used to identify five distinct phylogenetic clades. Our data showed that disease pathogenesis cannot be determined through phylogenetic relationships but can be determined by genes encoded by plasmids. We examined 51 plasmids from 10 C. perfringens strains, and categorised each plasmid into one of five plasmid families, which we designated as the Pcp, Tcp, Bcp, pIP404 or unclassified families. Within all 453 genomes in this study, a further 1007 plasmid-encoding contigs were extracted. Through this analysis we identified the first non-conjugative cpe-encoding plasmids, and a putative novel conjugative locus (Bcp) that was similar to a conjugation locus seen in Clostridium botulinum plasmids. We have expanded the C. perfringens genome collection including strains from each toxinotype and used this to confirm the presence of five distinct phylogenetic clades. Furthermore, novel plasmids were identified which expand the number of conjugation loci and cpe-encoding plasmids characterised within C. perfringens.