Phytopathogens threaten natural ecosystems and global food security. Horticultural trade is the main long-distance pathway causing the spread of these organisms and disease outbreaks worldwide. Most inspections for disease symptoms are conducted visually but this is insufficient given the large number of plants and the prevalence of asymptomatic infections. Therefore, there is increasing interest in the use of high-throughput sequencing (HTS) and environmental DNA (eDNA) for plant health surveillance. Many studies have used these technologies to detect phytopathogens, but fewer have done so in horticultural settings. Furthermore, much work has focused on the molecular and bioinformatic approaches for this work, with relatively little attention given to sample collection. This systematic review therefore provides an overview of the available sampling methods and their target plant pathogens, with a particular focus on the utility of these sampling methods in horticultural nurseries. It highlights some striking gaps in the literature and opportunities for further research, for example, the detection of bacterial phytopathogens using eDNA has received little attention despite having considerable potential as a surveillance and/or diagnostic tool.