Plasmids provide an important vehicle to disseminate antimicrobial resistance (AMR), imposing a challenge for global infection. Many plasmids, including those of the IncA/C subtype, have the ability to transfer AMR genes among diverse bacterial hosts and thereby disseminate resistance to antibiotics. No molecular typing methods are yet available to understand the epidemiology of IncA/C plasmids. High-throughput sequencing (HTS) is increasingly cheap and captures both chromosomal and plasmid DNA, however methods for identifying and analysing plasmid sequences from HTS data are lacking. We investigated how HTS data can be used to analyse IncA/C plasmid diversity and distribution amongst Gram-negative bacteria; and whether different subtypes of IncA/C plasmids are associated with specific bacterial host species or geographical regions. We identified 28 completely sequenced IncA/C plasmids in the NCBI database and screened these against the genes (n=160) of the reference IncA/C plasmid pRA1, to determine the conservation of these genes among the IncA/C plasmid population. In addition, we assembled and screened 1,672 Gram-negative bacterial genomes, sequenced via Illumina (including in-house and publicly available data) to identify novel IncA/C plasmids. A total of 23 novel IncA/C plasmids were detected. We collated the metadata of the respective host bacteria, analysed all 51 IncA/C plasmids and identified 10 core genes (present in all 51 plasmids) and 54 common genes (present in ≥90% of the IncA/C plasmids). Finally, we used short-read mapping to these 54 common genes to identify plasmid SNPs, and inferred a maximum likelihood phylogenetic tree using RaxML. The analysis showed two distinct IncA/C plasmid lineages: one common lineage that was widely geographically distributed (45 plasmids, detected in 15 countries) and one rare lineage (6 plasmids, detected only in 3 Asian countries). This approach will be useful for investigating the host and geographic distribution of IncA/C plasmids, as well as detecting and tracking other plasmid types.