Globally, the anaerobic bacteriumClostridium perfringenscauses severe disease in a wide array of hosts; however,C. perfringensstrains are also carried asymptomatically. Accessory genes are responsible for much of the observed phenotypic variation and virulence within this species, with toxins frequently encoded on conjugative plasmids and many isolates carrying up to 10 plasmids. Despite this unusual biology, current genomic analyses have largely excluded isolates from healthy hosts or environmental sources. Accessory genomes, including plasmids, also have often been excluded from broader scale phylogenetic investigations. Here we interrogate a comprehensive collection of 464C.perfringensgenomes and identify the first putative non-conjugative enterotoxin (CPE)-encoding plasmids and a putative novel conjugative locus (Bcp) with sequence similarity to a locus reported fromClostridium botulinum. We sequenced and archived 102 newC. perfringensgenomes, including those from rarely sequenced toxinotype B, C, D and E isolates. Long-read sequencing of 11C.perfringensstrains representing all toxinotypes (A–G) identified 55 plasmids from nine distinct plasmid groups. Interrogation of the 464 genomes in this collection identified 1045 plasmid-like contigs from the nine plasmid families, with a wide distribution across theC. perfringensisolates. Plasmids and plasmid diversity play an essential role inC. perfringenspathogenicity and broader biology. We have expanded theC. perfringensgenome collection to include temporal, spatial and phenotypically diverse isolates including those carried asymptomatically in the gastrointestinal microbiome. This analysis has resulted in the identification of novelC. perfringensplasmids whilst providing a comprehensive understanding of species diversity.