The microbiome of agricultural crops influences processes such as nutrient absorption, drought stress, and susceptibility to pathogens. Interactions between a plant’s genotype and its environment influence the composition of the microbiome, but these interactions are not well understood. We compared how the fungal and oomycete microbiomes of rhododendrons from Oregon nurseries differed among cultivars, growth conditions, and nurseries. Roots were sampled from randomly selected container and field-grown plants of three cultivars of rhododendron at four nurseries. The internal transcribed spacer 1 (ITS1) barcode was sequenced with the Illumina MiSeq using two sets of primers specific to fungi and oomycetes, respectively. Sequences were used to infer community composition using VSEARCH and a custom reference database combining curated fungal and oomycete sequences. Comparisons of diversity and community composition were conducted in R using the vegan and metacoder packages. Organism lifestyle was inferred using the FUNGuild database. Few oomycetes were found and fungal communities were dominated by saprobes and mutualists. Nurseries that grew plants in containers and in-field had a significantly higher diversity of fungi than those that only grew plants in containers. Microbiome composition differed significantly among growth conditions and nurseries, but not among cultivars. This suggests that, among these cultivars of rhododendron, environment is important in structuring the root microbiome, but cultivar is not.