Although plant adaptation to serpentine soils has been studied for several decades, the mechanisms of plant adaptation to edaphic extremes are still poorly understood. Arbuscular mycorrhizal fungi (AMF) are common root symbionts that can increase the plant hosts’ establishment and growth in stressful environments. However, little is known about the role plant–AMF interactions play in plant adaptation to serpentine. As a first step towards understanding this role, we examined the AMF assemblages associated with field populations of serpentine and non-serpentine ecotypes of California native plant Collinsia sparsiflora. We sampled roots of C. sparsiflora from three serpentine and three non-serpentine sites in close proximity (110 m to 1.94 km between sites) and analysed the small subunit ribosomal DNA gene amplified from root DNA extracts using AMF-specific primers. A total of 1952 clones from 24 root samples (four from each site) were sequenced. We used sequence similarity and phylogenetic analysis to determine operational taxonomic units (OTU) resulting in 19 OTUs representing taxa from six AMF genera, including one serpentine-specific OTU. We used Bray–Curtis similarity, multidimensional scaling and analysis of similarity to compare root sample AMF assemblages. These analyses clearly showed that plant ecotypes associated with distinct AMF assemblages; an Acaulospora OTU-dominated serpentine, and a Glomus OTU-dominated non-serpentine assemblages. Species diversity and evenness were significantly higher in serpentine assemblages. Finally, relate analysis showed a relationship between ecotype AMF assemblages and soil nutrients. This study reveals a strong relationship between AMF associates and plant adaptation to edaphic extremes.