Phytophthora ramorum causes sudden oak death throughout the American west coast, where it infects tan oak, live oak, and bay laurel, as well as the UK, where it infects Japanese larch. Copy number variation (CNV) has been implicated as contributing to pathogenic phenotypes in clonal pathogens including P. ramorum, but it has not been determined how extensive CNV may be in P. ramorum populations. In order to explore this topic we first updated the genomic reference by sequencing Pr-102 using Pacific Biosciences technology. We then downloaded 189 read libraries from the SRA and sequenced 11 genomes from southern Oregon to explore copy number variation within three of the clonal lineages (NA1, NA2, EU1) as well as variation in southern Oregon. The updated reference resulted in a 75,183,546 bp assembly with no gaps, over 20 Mbp longer than the reference produced by the JGI using Sanger sequencing which was shorter and contained gaps. The assembly had a N50 of 1,287,631 indicating the fewer contigs were longer than the JGI reference that had a N50 of 308,042. While most isolates were observed to be predominantly diploid, copy numbers of three, four, and possibly five were observed for large contiguous regions in many but not all strains. CNV may thus be the predominant form of genetic diversity generation in clonal lineages. Our results suggest that CNV occurs in almost all lineages of P. ramorum and may play an important role in P. ramorum epidemics worldwide.