Xylella fastidiosa (Xf) is a vector-transmitted, xylem-limited bacterium native to the Americas. It causes devastating plant diseases such as Pierce’s disease on grapes, Citrus Variegated Chlorosis, and Olive Quick decline syndrome, among others. It has mainly been confined to the Americas for thousands of years, but recently, it has been detected in other locations such as Europe and China. New Zealand (NZ) and Australia currently are free of Xf. We have recently demonstrated that several NZ indigenous plants, both woody and non-woody, can harbour the bacterium; we screened the NZ plant collections held in several Botanic Gardens in Southern California and the University of California Berkeley Botanic Gardens, showing the applied value of botanical garden collections as sentinels for international plant pathogen risk assessment (1,2). Using samples sourced from these plant collections, we have evaluated Nanopore sequencing from Oxford Nanopore Technologies (ONT) for the detection of Xf using a shotgun metagenomics approach. Results obtained by this method were compared with those from the main qPCR assay used for Xf detection. An assessment of using ONT for multiple plant pathogen detection in a single assay will be also discussed. As part of this work, the official list of NZ native plant hosts harbouring Xf will be updated. This information would be vital during a potential Xf incursion in NZ to inform the containment and eradication strategy.