Genome data for 25 isolates of the prevalent forest and nursery pathogen, Phytophthora cinnamomi, from New Zealand

<i>Phytophthora cinnamomi</i> is a globally distributed plant pathogen with a remarkably broad host range. It is considered one of the greatest threats to natural and productive ecosystems, especially under changing climatic conditions. In New Zealand, this pathogen has been present for a long time, but the genetic diversity is not well understood. We describe here draft genome assemblies for 25 isolates of <i>P. cinnamomi</i> from New Zealand trees, forests and nurseries. The genome assembly data showed an average size of 129 MB with an average N90 value of 297,992 bp. This data will enable the analysis of genetic diversity of New Zealand <i>P. cinnamomi</i> isolates, and the development of accurate detection and diagnostic tools.